Release notes and usage changes

Updates from previous releases

Release 202503.02

Type	Description
Feature	Introduced β-version of Pangenome pipeline with accelerated alignment.
Feature	Improved InsertSizeMetricAlgo to include single-end consensus reads in the insert size metrics calculation.
Bug-fix	Solved issue in GVCFtyper that caused a third-party tool fail when InbreedingCoeff is -nan.
Bug-fix	Solved issue in Consensus Dedup that caused a segmentation fault when the input is RNA reads with UMI.
Bug-fix	Solved issue in TNscope with PoN filtering that incorrectly filtered variants based on locus.
Bug-fix	Removed unnecessary environment variables in plot.

Release 202503.01

Type	Description
Feature	Improved DNAscope model apply speed substantially.
Bug-fix	Solved issue in TNscope that could call a false positive in somatic amplicon data.
Bug-fix	Solved issue that could produce malformed CRAM file under rare circumstances.
Bug-fix	Solved issue in Consensus-based Dedup that could cause an assertion failure when the input is RNA reads with UMI.
Bug-fix	Solved issue in DNAscope that caused a segmentation fault when a machine learning model is used on a non-human sample.

Release 202503

Type	Description
Feature	Added support for hybrid short and long-read variant calling.
Feature	Added support for reading and writing CRAM version 3.1 files.
Feature	Added support in GVCFtyper algorithm for joint calling DNAscope GVCFs from long reads pipeline.
Feature	Added support in TNscope algorithm to output FAD, F1R2, and F2R1 annotations.
Feature	Added option in GCBias and AlignmentStat algorithms to match with Picard IS_BISULFITE_SEQUENCED option.
Feature	Reduced memory utilization in HsMetricAlgo algorithm.
Bug-fix	Solved issue in driver where minor inconsistencies in alignment @SQ records can cause an error.
Bug-fix	Solved issue in consensus Dedup where paired consensus reads may not have matching read names.
Bug-fix	Solved issue in LongReadSV algorithm that could cause a crash under rare circumstances.
Bug-fix	Solved issue in DNAscope and Haplotyper that could cause an assertion when using the –bam_output option.
Bug-fix	Solved issue in consensus Dedup that would cause the job to hang when –metrics is turned on.
Bug-fix	Solved issue in TNhaplotyper2 in given mode that may produce incorrect results.
Bug-fix	Solved issue in TNscope that missed low-AF variants at the site of germline homozygous variants.
Other	Removed umi consensus from the software package.
Other	Removed gnuplot binary from the software package.

Release 202308.03

Type	Description
Feature	Support STAR for ARM based CPUs.
Feature	Support minimap2 for ARM based CPUs.
Feature	Optimized performance of DNAModelApply on some newer ARM CPUs.
Feature	Added read filter SimplifyCigarTransform to simplify and standardize cigars.
Feature	Added support for consensus and UMI-aware deduplication metrics in Dedup.
Bug-fix	Solved issue in util sort to handle empty type Z and type H tags in input SAM records.
Bug-fix	Solved some phasing issues in the long-reads DNAscope pipeline.
Bug-fix	Solved potential stack overflow issue when input bam depth is extremely high.

Release 202308.02

Type	Description
Feature	Added support in Haplotyper algorithm to output RAW_MQandDP annotation.
Feature	Added support in GVCFtyper algorithm for gVCFs containing the RAW_MQandDP annotation.
Bug-fix	Solved an issue in GVCFtyper that could cause an assertion when input gVCF file’s tbi index is from third-party tool.
Bug-fix	Solved issue in GVCFtyper that could cause a segmentation fault when input gVCF file is from CombineGVCFs.
Bug-fix	Solved issue in TNscope that may miss large INDELs in single-end sequencing data.

Release 202308.01

Type	Description
Feature	Added support in TNhaplotyper2 algorithm to run in distributed mode.
Feature	Added support in ContaminationModel algorithm to run in distributed mode.
Feature	Added support in OrientationBias algorithm to run in distributed mode.
Feature	Added support for CSI index for compressed VCF files.
Feature	Maintenance update of GeneEditEvaluator.
Feature	Added better error message in util sort when input fastq to aligner is not legitimate.
Bug-fix	Solved issue in Haplotyper that could cause an error when using the –bam_output option.
Bug-fix	Solved issue in TNscope where variants may report incorrect annotations under rare circumstances.
Bug-fix	Solved issue in LongReadSV that failed to report variants in non-canonical chromosomes.
Bug-fix	Solved issue in util sort when –output_format CRAM is used without a reference.

Release 202308

Type	Description
Feature	Improved DNAscope pipeline speed and accuracy with a BWA model.
Feature	Improved long-reads DNAscope pipeline speed and accuracy with minimap2 models.
Feature	Improved speed of STAR when input format is SAM.
Feature	Improved speed of deduplication on RNA data.
Feature	Improved consensus based deduplication and UMI barcode aware deduplication for RNA data.
Feature	Improved consensus of INDELs in Dedup algorithm.
Feature	Improved speed of DNAscope on long-reads small variant call.
Feature	Improved machine learning model for TNscope.
Feature	Introduced LongReadUtil to extract cell barcode from Oxford Nanopore single-cell RNA data.
Feature	Introduced α-version of GeneEditEvaluator algorithm for genome editing sequence analysis.
Feature	Added support in Dedup to handle INDEL errors in barcode.
Feature	Added support to encapsulate multiple machine learning models into a single file.
Feature	Added support in GVCFtyper to output PL and ML FORMAT fields.
Feature	Added support in umi extract to output SAM format.
Feature	Added support for small variant calling on Oxford Nanopore data.
Feature	Maintenance update of STAR.
Feature	Maintenance update of minimap2.
Feature	Reduced memory utilization in util sort for long reads.
Bug-fix	Solved an issue in umi consensus that could cause an assertion failure under rare circumstances.
Bug-fix	Solved issue in DNAscope that may filter softclip reads at high coverage sites.

Release 202112.07

Type	Description
Feature	Introduced β-version of consensus based deduplication and UMI barcode aware deduplication for RNA data.
Bug-fix	Solved an issue in Dedup that could cause an assertion failure when the output format is CRAM.
Bug-fix	Solved issue in util sort to handle type B tags in input SAM records.
Bug-fix	Improved license server fault tolerance upon extreme high usage demand.

Release 202112.06

Type	Description
Feature	Added support in LocusCollector and Dedup algorithms to perform consensus based deduplication as well as UMI barcode aware deduplication.
Feature	Added support in Dedup algorithm to perform UMI barcode error correction.
Feature	Added support in GVCFtyper for joint calling DNAscope GVCFs from multiple sequencing platforms into a single multi-sample VCF.
Feature	Added support in GVCFtyper for gVCF files without PL fields.
Feature	Added support in LongReadSV algorithm to process Oxford Nanopore long reads in addition to PacBio HiFi long reads.
Feature	Improved TNscope SV to better handle different representations of the same alignment.
Bug-fix	Solved issue in umi consensus that could cause a segmentation fault when input has 0-length read.
Bug-fix	Solved issue in GVCFtyper that would produce <NON_REF> alleles under rare circumstances.
Bug-fix	Solved issue that Plot GCBias was left-shifted on some datasets.

Release 202112.05

Type	Description
Feature	Maintenance update of UltimaReadFilter.
Feature	Added option in TNscope to control adapter trimming.
Feature	Added environment variable in bwa mem for bug compatibility.
Feature	Added wrapper script for STAR in the bin directory to remove the requirement of setting LD_LIBRARY_PATH.
Bug-fix	Solved issue in STAR that printed out extra information with the argument –version.
Bug-fix	Solved issue in duplex umi consensus that could output zero-length reads.
Bug-fix	Solved issue in umi consensus that slowed down execution under rare circumstances.
Bug-fix	Solved issue in TNscope such that evidence from overlapping read pairs were not adequately accounted for.

Release 202112.04

Type	Description
Feature	Added support for DNAscope with machine learning model to generate gVCF file for subsequent joint call.
Feature	Introduced β-version of LongReadSV algorithm to perform germline structure variant call for long reads.
Feature	Added options in InsertSizeMetricAlgo to control the threshold to output FR, TANDEM, RF.
Feature	Maintenance update of read filter.
Feature	Improved reference assembly detection logic.

Release 202112.02

Type	Description
Feature	A license framework to support multiple sequencing platforms.
Feature	Improved bwa-mem speed on certain ARM CPU.
Bug-fix	Solved issue in GVCFtyper that would produce no-calls in certain ploidies when input is a multi-sample merged gVCF from third party tool.
Bug-fix	Solved issue in DNAscope that could produce no call at zero coverage site when using –given.
Bug-fix	Solved issue that triggered CRAM buffer overflow when minimap2 output zero-length secondary reads.
Bug-fix	Solved issue in minimap2 that would cause the job to hang under rare circumstances.

Release 202112.01

Type	Description
Feature	Improved accuracy of DNAscope machine learning model compared to NIST truth-sets v4.2.1.
Bug-fix	Solved issue in TNscope that missed SNPs with 1% AF under very sensitive settings.
Bug-fix	Solved issue in TNscope that failed to report variants when the sequence length is shorter than 30bp.
Bug-fix	Solved issue in TNscope that could report incorrect AF number for Amplicon data.
Bug-fix	Solved issue in umi consensus that could cause a crash under rare circumstances.
Bug-fix	Added additional error checks and error reporting in util sort.

Release 202112

Type	Description
Feature	Improved speed of bwa mem.
Feature	Improved speed of minimap2 when -x splice:hq argument is used.
Feature	Improved speed of LocusCollector when input bam has huge number of contigs.
Feature	Implemented a low memory usage mode for extremely large GVCFtyper jobs.
Feature	Added option in TNhaplotyper2 to match with GATK –genotype-germline-sites option.
Feature	Added ELEMENT platform to support Element Biosciences sequencers.
Feature	Modified TNscope® AF output format.
Feature	Added support in GVCFtyper to take multi-sample gVCF files with coverage gaps.
Bug-fix	Solved matching issue in STAR when using non-default value for chimMultimapNmax.
Bug-fix	Solved buffer overflow issue in STAR due to base count difference between input R1 and R2.
Bug-fix	Solved issue in TNhaplotyer2 that could cause matching difference with GATK-4.2.0.0 when the input bam has high QUAL N bases.
Bug-fix	Solved issue in TNhaplotyper2 that could cause a crash under rare circumstances.
Bug-fix	Solved minor matching issue in median annotations in TNhaplotyper2.
Bug-fix	Solved issue that triggered stack overflow when input bam has substantially dense region.
Bug-fix	Solved issue in duplex umi consensus that results depend on internal data order.
Bug-fix	Added additional error checks and error reporting.

Release 202010.04

Type	Description
Feature	Improved speed of Minimap2.
Feature	Mantainance update of Minimap2
Bug-fix	Solved issue in VariantPhaser that could cause a crash under rare circumstances.
Bug-fix	Solved issue in VariantPhaser that could output variants out of order.
Bug-fix	Solved issue in DNAscope that could cause an error when running with HiFi data.
Bug-fix	Reduced memory utilization in DNAscope when using HiFi data aligned with minimap 2.22.
Bug-fix	Added additional error checks and error reporting.
Bug-fix	Updated sentieon wrapper to default to use python system binary, then python3 and last python2.

Release 202010.03

Type	Description
Feature	Introduced β-version of PacBio HiFi reads pipeline.
Feature	Introduced β-version of VariantPhaser tool to do read-based phasing for long reads.
Feature	Introduced β-version of minimap2 aligner for PacBio and Nanopore reads.
Feature	Added support in the sentieon wrapper to run Sentieon python scripts.
Bug-fix	Added additional error checks and error reporting.

Release 202010.02

Type	Description
Feature	Maintenance update of the TNseq algorithm.
Feature	Added support in util for amplicon specific primer clipping.
Feature	Added support to access s3 objects from a region different than the one hosting the bucket.
Feature	Improved speed of TNhaplotyper2 for extreme depth cases.
Feature	Introduced β-version of STAR aligner.
Bug-fix	Solved an issue when using CRAM files that could incorrectly report reads as missing the RG under very rare circumstances.
Bug-fix	Solved issue in CoverageMetrics that could cause a small run-to-run results difference.
Bug-fix	Solved issue when using CRAM that could drop certain malformed reads from output.
Bug-fix	Solved issue in TNhaplotyper2 that could cause an error when using the –bam_out option.
Bug-fix	Solved issue in TNfilter that would cause an error when encountering unrecognized reference bases.
Bug-fix	Solved issue in util sort –umi_post_process that would cause an incorrect BI/BD tag.
Bug-fix	Solved issue when reading BAM files with convoluted PGs that would cause a crash.
Bug-fix	Solved issue in TNhaplotyper, TNhaplotyper2 and TNscope that could cause a crash when using options –given and –bam_output.
Bug-fix	Solve issue in TNhaplotyper2 that could produce incorrect PS values.
Bug-fix	Solved issue in some metrics algorithms that was producing trailing tabs causing an empty column output.
Bug-fix	Added additional error checks and error reporting.

Release 202010.01

Type	Description
Feature	Added support in TNhaplotyper2 for genotyping given alleles.
Feature	Improved TNscope® method for handling read trimming.
Feature	Added support in TNscope® for amplicon specific primer removal.
Bug-fix	Added additional error checks and error reporting.
Bug-fix	Fixed issue in TNscope® that could report incorrect AD numbers at tri-allelic sites.
Bug-fix	Solved issue in ContaminationModel that could calculate incorrect estimates when using very sparse pileups.
Bug-fix	Solved issue in Haplotyper that could cause a crash for inputs with high depth close to the start of a non-canonical chromosome.
Bug-fix	Solved issue in umi consensus that could cause the sequence and BI/BD to be inconsistent when using duplex UMI.
Bug-fix	Solved issue in ContaminationModel that could cause a crash under rare circumstances.
Bug-fix	Solved issue that could cause a crash when using the Sentieon® libraries with bcl2fastq.

Release 202010

Type	Description
Feature	Reduced memory usage when outputting CRAM files.
Feature	Maintenance update of the TNseq algorithm.
Feature	Added DNBSEQ platform to support BGI sequencers.
Feature	Improve speed of umi consensus when not outputting BI/BD tags.
Feature	Added support of BGZF compressed interval list files as well as VCF and VCF.gz files.
Feature	Modified the type of the AD, QSS and RPA FORMAT field in the VCF.
Feature	Override unlimited stack size limit in Linux to prevent Linux bug with thread local storage allocation.
Feature	Using an empty interval bed file will result in no processing done, as if the interval had 0 length.
Bug-fix	Added additional error checks and error reporting.
Bug-fix	Solved issue that would cause a crash when using BAM files containing reads without a sequence.
Bug-fix	Added option in util sort to handle supplementary reads after processing with the umi tools.
Bug-fix	Solved issue in umi consensus that could cause results to depend on the number of threads.
Bug-fix	Solved issue in Haplotyper that could cause an out of bound memory access error in very rare circumstances
Bug-fix	Solved issue in util sort that could cause it to hang for single threaded jobs under very rare circumstances.
Bug-fix	Solved issue in umi consensus that could cause a segmentation fault.
Bug-fix	Solved issue in umi consensus that produced a non informative group 0 histogram when using –min_reads 1.
Bug-fix	Error out when creating CRAM file containing reads beyond the reference end.
Bug-fix	Solved issue in plot that would not respect the SENTIEON_TMPDIR environmental variable.

Release 201911.01

Type	Description
Feature	Reduced number of temporary files in util sort.
Feature	Improved UMI consensus calculation for INDELs.
Feature	Reduced memory usage in UMI tool.
Feature	Added support in umi extract to read FASTQ files containing UMI tags already extracted.
Feature	Added support in Dedup metrics to report QCFAIL reads if present.
Feature	Made the rsID field population from dbSNP more robust.
Bug-fix	Solved issue that would cause a crash when using CRAM files and unmapped reads of zero length.
Bug-fix	Solved issue in SequenceArtifactMetricsAlgo that could cause a negative result.
Bug-fix	Solved issue in BWA that could cause an error when using a value larger than 520g for bwt_max_mem option.
Bug-fix	Solved issue in the vcflib python library that could cause an error processing VCFs from SVSolver
Bug-fix	Added additional error checks and error reporting.
Bug-fix	Solved issue in umi extract that could cause a crash.
Bug-fix	Solved issue that could slow down merging of large output files.
Bug-fix	Solved issue that could generate an incorrect CRAM index file when a slice contained multi contigs.
Bug-fix	Solved issue in licsrvr for Mac that could prevent it from stopping when running the –stop command.
Bug-fix	Solved issue that could cause a crash when using CRAM files and reads longer than 128KBases.
Bug-fix	Solved issue in util sort that could cause a crash with very large SAM records.
Bug-fix	Solved issue in Haplotyper that could cause an out of bound memory access error in very rare circumstances
Bug-fix	Solved issue in DNAscope that could produce no GT when using –given.
Bug-fix	Solved issue in CollectVCMetrics that could cause incorrect results for INDELs straddling beyond the input interval.

Release 201911

Type	Description
Feature	Introduced β-version of tools for processing reads containing UMI sequences.
Feature	Introduced β-version of software for ARM based CPUs.
Feature	Added support in ReadWriter to filter reads based on the mapping quality.
Feature	Maintenance update of BWA
Feature	Improved speed of util sort on high CPU count servers.
Feature	Added support in ReadWriter to filter reads based on their flags.
Feature	Added support to GVCFtyper to output very small AF numbers in scientific notation.
Feature	Modified the type of the AD FORMAT field in the VCF.
Feature	Added support in TNscope® to output ID and MATEID in its BND output.
Bug-fix	Solved issue in VarCal that could cause a numeric overflow
Bug-fix	Solved issue in Haplotyper that could cause a segmentation fault under very rare circumstances.
Bug-fix	Solved issue in TNscope® calling SVs that would output an invalid AD value for the normal sample, if present.
Bug-fix	Solved issue in DNAscope that would prevent generating a GVCF when using sharded mode.
Bug-fix	Solved issue in VarCal that would cause an issue when using a VCF containing an INF value annotation.
Bug-fix	Solved issue in Haplotyper and DNAscope that would not trim common bases in REF and ALT in a variant with a spanning delete.
Bug-fix	Solved issue in TNscope® SV calling that could shift the position by a few bases under rare circumstances.
Bug-fix	Solved issue in GVCFtyper that would create a SOR=nan for large cohorts
Bug-fix	Solved issue in the DNAscope Smith-Waterman that could cause a results difference in very rare circumstances.
Bug-fix	Solved issue that could cause an error when inputing sharded VCF files indexed by other tools.
Bug-fix	Added additional error checks and error reporting.

Release 201808.08

Type	Description
Bug-fix	Solved issue in Haplotyper that could create an incorrect tbi index file.
Bug-fix	Solved issue in DNAscope and Haplotyper that could cause an assertion when using the –bam_output option.
Bug-fix	Solved issue in LocusCollector that could cause an assertion when creating a compressed score file.

Release 201808.07

Type	Description
Feature	Improved speed of QualCal on high CPU count servers.
Feature	Improved speed of Dedup on high CPU count servers.
Feature	Improved speed of GVCFtyper merge for large cohorts.
Bug-fix	Solved issue preventing reading CRAM files with slices straddling across multiple contigs; the Sentieon® tools do not generate such CRAM files.
Bug-fix	Added additional error checks and error reporting.
Bug-fix	Solved issue that would cause an error when using BAM files containing incomplete PG records.
Bug-fix	Solved issue in GVCFtyper that would cause an error when using phased GT annotation.

Release 201808.06

Type	Description
Bug-fix	Solved issue in GVCFtyper that could cause an error when using multinomial genotyping and more than 1000 samples.

Release 201808.05

Type	Description
Feature	Improved speed of BWA alignment.
Feature	Changed default CRAM output version to 3.0
Feature	Reduced memory usage when outputting CRAM files.
Feature	Added error checking in tnhapfilter.
Feature	Improved accuracy of DNAscope model.
Feature	Removed Realigner stages from the example files
Feature	Added option in Haplotyer and GVCFtyper to use additional genotyping models.
Bug-fix	Solved issue in TNhaplotyer2 that could cause a run to run variation in the annotation calculation in 1 out of 100 runs.
Bug-fix	Solved issue in BWA that could cause an error when using an extremely large bwt_max_mem option.
Bug-fix	Solved issue that could cause an error when reading a CRAM file generated by cramtools.
Bug-fix	Improved error reporting.

Release 201808.03

Type	Description
Bug-fix	Solved issue in TNscope® that set the wrong default settings.

Release 201808.02

Type	Description
Feature	Improved speed of TNscope®.
Feature	Added option –trim_soft_clip to TNscope®, TNhaplotyper and TNhaplotyper2.
Feature	Added capability for output BAM from –bam_output option to keep the input BAM RG information.
Feature	Added option –disable_detector to TNscope® to control the type of variants called.
Feature	Added support in TNscope® SV calling to more accurately represent large INS.
Feature	Added mode to util fqidx to extract a fraction of the reads.
Feature	Added support in GVCFtyper merge mode to allow input files hosted in an object storage location.
Feature	Added support for using multiple –interval options.
Bug-fix	Solved issue in TNscope® that could call a false positive in a site that has a germline call and is neighboring another SNV.
Bug-fix	Improved error reporting.
Bug-fix	Solved issue in sentieon script that could prevent using a demo license on a shell that is not BASH.
Bug-fix	Solved issue that would prevent BED files containing an interval with identical start and end.
Bug-fix	Solved issue in DNAModelApply that would cause an error when the input VCF file is empty.
Bug-fix	Solved issue in plot that could cause it to run longer than necessary.
Bug-fix	Solved issue in DNAModelApply that would cause an error when over-scheduling.
Bug-fix	Solved issue in util sort that could cause an assertion error when over-scheduling.
Bug-fix	Solved issue in plot that would generate BQSR PDF plots without AA and AAA context covariate.

Release 201808.01

Type	Description
Feature	Improved performance of DNAscope and Machine learning model
Feature	Improved speed of Insert Size plotting when the sample has very large insert sizes
Bug-fix	Solved issue in GVCFtyper that could create a non conforming VCF when doing joint calling of DNAscope results.
Bug-fix	Solved issue in DNAModelApply that would cause an error when the input file does not contain a ModelID.
Bug-fix	Solved issue in Haplotyper when using the –given option that would generate a VCF without the LowQual filter definition in the header.
Bug-fix	Solved issue in tnhapfilter tool to include tumor sample in the header of the VCF

Release 201808

Type	Description
Feature	Added support in ReadWriter for customized flag read filters.
Feature	Added support to modify the read group information of an input BAM file.
Feature	Added support in TNscope® and TNhaplotyper to output a BAM including local reassembly of the reads.
Feature	Added support in TNModelApply to include command line to the VCF output.
Feature	Added support to QualCalFilter to keep the base quality scores before recalibration.
Feature	Introduced TNhaplotyper2 algorithm
Feature	Added support for outputting CRAM v 3.0 files.
Feature	Added support in Haplotyper, DNAscope and GVCFtyper to input the expected heterozygosity value used to compute prior likelihoods.
Feature	Updated interface of plot to better match other tools.
Feature	Added support for machine learning model for DNAscope
Feature	Modified the help for driver options to make it more user friendly.
Feature	Improved speed in Dedup.
Feature	Added support in Haplotyper, Genotyper and DNAscope to include @PG line in the output header of the `--bam_output` argument.
Feature	Updated the @PG information when processing in distribution mode to make it more informative.
Bug-fix	Solved issue in GVCFtyper on DNAscope GVCFs that may report incorrect phasing on a multi-allelic variant
Bug-fix	Solved issue in util sort that would cause an error in older CPUs.
Bug-fix	Added additional error checks and error reporting.
Bug-fix	Solved issue in LocusCollector that would cause a crash when running 2 commands in parallel outputting to the same file.
Bug-fix	Solved issue in Haplotyper that could create a GVCF with REF allele incorrectly set to N under very rare conditions.
Bug-fix	Solved issue in TNscope® that may use uninitialized values
Bug-fix	Solved issue in AlignmentStat that would report an incorrect command line in the header of the output file.
Bug-fix	Solved issue that could slow down the startup when the LIBDIR contains many files and is stored in a NFS.

Release 201711.05

Type	Description
Bug-fix	Solved issue in in Haplotyper that could create a GVCF file that does not cover the entire region under rare circumstances.

Release 201711.04

Type	Description
Feature	Added support to all BAM writing tools to preserve existing PG tags in the header.
Bug-fix	Solved issue in TNscope® that could cause an error with references containing small contigs.
Bug-fix	Solved issue in SVSolver that could cause a segmentation fault.
Bug-fix	Solved issue in Haplotyper when using the —bam_output option that could generate a debug BAM file incompatible with other tools.
Bug-fix	Solved issue in ApplyVarCal that would generate a non-compliant list of FILTERs if the input file already had existing filters.

Release 201711.03

Type	Description
Feature	Reduced memory usage in GVCFtyper.
Feature	Improved the speed of BWA alignment.
Feature	Added command line to output of metrics tools.
Feature	Reduced memory usage in util sort.
Feature	Reduced TNscope® SV calling runtime for very large samples.
Bug-fix	Solved issue in GVCFtyper merge when using `--split_by_sample` that would cause an error in merging files with a large number of samples.
Bug-fix	Solved issue in WgsMetricsAlgo that would cause an error under very rare circumstances.
Bug-fix	Reduced memory usage in WgsMetricsAlgo and SequenceArtifactMetricsAlgo tools.
Bug-fix	Solved issue in SequenceArtifactMetricsAlgo that would produce an error when using reference FASTA files with non-ACGT bases.
Bug-fix	Solved issue in WgsMetricsAlgo that would cause an error when the `--coverage_cap` argument is not within the valid rage.
Bug-fix	Solved issue in SequenceArtifactMetricsAlgo that would cause an error when the `--context_size` argument is not within the valid rage.

Release 201711.02

Type	Description
Feature	Added support for BWA shm mode.
Feature	Added QC metrics tools: BaseDistributionByCycle, QualityYield, WgsMetricsAlgo, SequenceArtifactMetricsAlgo.
Feature	Improved speed in TNscope® when calling SVs.
Feature	Added support in TNscope® to show progress report during the SV calling.
Feature	Reduced memory usage in TNscope® while calling SVs.
Feature	Introduced β-version of Windows based tools.
Feature	Improved speed for the Windows version.
Feature	Added additional error checks and error reporting.
Feature	Modified the default behavior in DNAscope when only calling short variants to filter out chimeric reads during genotyping.
Feature	Reduced memory usage in GVCFtyper.
Bug-fix	Solved issue in Haplotyper that would cause an error if the input BAM file contained reads where the cigar is composed solely of soft and hard clips.
Bug-fix	Solved issue in TNscope® that could cause a segmentation fault when using an incomplete BAM file.
Bug-fix	Solved issue in TNscope® that would cause a segmentation fault under rare circumstances.
Bug-fix	Solved issue in Haplotyper and DNAscope that could cause an error when using the `bam_output` option.
Bug-fix	Solved issue in Realign that would not do the proper read pairing when dealing with secondary alignments.
Bug-fix	Maintenance update on the SVsolver algorithm.
Bug-fix	Solved issue in licsrvrv for Windows that would prevent it from working with HTTP proxy servers with authentication.
Bug-fix	Solved issue in GVCFtyper that would produce VCF records with non-conformant MQ0 when the input GVCFs include MQ0 annotation.

Release 201711.01

Type	Description
Feature	Improved QualCal speed for very small jobs.
Feature	Added support in licsrvr to report the version.
Feature	Added support in licsrvr to report an update in the license.
Bug-fix	Solved issue in licsrvr that would prevent from working HTTP proxy servers that return auth schemes in multiple header lines.
Bug-fix	Solved issue in Haplotyper, DNAscope, TNhaplotyper and TNscope® that could cause an “illegal instruction” error in AWS.
Bug-fix	Solved issue in TNscope® that would produce and “Error in function boost” under rare conditions.
Bug-fix	Solved issue in util that would prevent running vcfconvert on a compressed vcf.gz file.
Bug-fix	Solved issue in Haplotyper and DNascope that could cause an error when using the `--bam_output` option.
Bug-fix	Reduced memory usage in Realigner.
Bug-fix	Solved issue in TNhaplotyper and TNscope® that could incorrectly filter a variant as present in the Panel of Normals when the variant is covered by a DEL present in the PoN.
Bug-fix	Changed emit_conf value in the sample scripts to use the default value.
Bug-fix	Solved issue in TNhaplotyper and TNscope® that could produce an assertion error when using a fractured bed file with small intervals close to each other.
Bug-fix	Solved issue in TNscope® that would prevent the job from finishing when prune_factor is set to 0.
Bug-fix	Solved issue in BWA that prevented it from working on certain older AMD cpus.

Release 201711

Type	Description
Feature	Added support in Haplotyper to output a BAM including the local reassembly of the reads.
Feature	Introduced β-version of new functionality for applying a Machine Learning model to help with variant filtration in TNscope®.
Feature	Introduced β-version of new functionality for Python based recipe creation to drive the Sentieon® tools.
Feature	Introduced β-version of new product DNAscope for germline variant calling and germline structural variant calling.
Feature	Added support for printing the command line to stderr log, usually as the first line, before the license check.
Feature	Added support in QualCal to calculate recalibration tables based on PU if present.
Feature	Added support in ApplyVarCal to use both SNP and INDEL models in a single command line.
Feature	Added additional error checks and error reporting.
Bug-fix	Solved issue in TNscope® SV that would cause an error if the input BAM file contained realigned reads with no matching bases.
Bug-fix	Solved issue that would cause a crash when using a BAM file containing reads with invalid mate tid.
Bug-fix	Solved issue in GVCFtyper that could cause a job to incorrectly think there are not enough licenses available when the communication to the license server is slow.
Bug-fix	Solved issue in TNscope® that failed to detect long INDELs under rare circumstances.
Bug-fix	Solved issue in ApplyVarCal that caused the output VCF file to miss the Sentieon® CommandLine in the header.
Bug-fix	Solved issue in TNscope® that prevented modifying the max_normalAlt_active option, which could cause loss of variants in areas of extreme depth.
Bug-fix	Solved issue in GCBias that would report results for a RG that did not contain any reads.
Bug-fix	Solved issue in util that would cause a crash when the BAM contained reads whose tid is out of bound.
Bug-fix	Solved issue in util stream that would not include the full path of util binary in the PG line of the BAM header.
Bug-fix	Solved issue in AlignmentStat that would produce an inaccurate PCT_ADAPTER value when the adapter_seq is not null.
Bug-fix	Solved issue in ApplyVarCal that would produce incorrect results when using sensitivity 0.
Bug-fix	Solved issue in the help of TNhaplotyper that would misrepresent the default pcr_indel_model.
Bug-fix	Solved issue in BWA that prevented it from working on certain older AMD cpus.
Bug-fix	Solved issue in InsertSizeMetrics that would generate a header using space instead of tab.

Release 201704.03

Type	Description
Feature	Added support for using a HTTP proxy with authentication.
Bug-fix	Solved issue that would prevent recalibration tables from older releases from being applied when the BAM file RGs have a defined PU.
Bug-fix	Solved issue in Realigner that could cause an error under extremely rare circumstances when reads in the input file have inconsistent information.
Bug-fix	Solved issue in TNscope® that could incorrectly error out when the tumor_contamination_frac parameter was set to 0.
Bug-fix	Solved issue that was preventing using BAM files with Contigs larger than 300M.

Release 201704.02

Type	Description
Feature	Added support in QualCal to allow input of `--cycle_val_max` parameter.
Bug-fix	Solved issue in Realigner when input BAM file has wrong MC tag type.
Bug-fix	Solved issue in TNhaplotyper in `--detect_pon` that would produce a non-compliant VCF.
Bug-fix	Solved issue in TNscope® in `--given` mode that would not report records on areas of 0 depth coverage.
Bug-fix	Solved issue in CoverageMetrics that would report the wrong cumulative_coverage_counts, coverage.statistics when input BAM has multipe different readgroups.
Bug-fix	Solved issue in InsertSizeMetricAlgo, GCBias and CoverageMetrics that could report the wrong results for extremely deep (600x) samples.
Bug-fix	Solved issue in QualCal where cycle_val_max parameter was not opened to user.

Release 201704.01

Type	Description
Feature	Added additional checks on the input BAM files.
Bug-fix	Solved issue in Dedup that would cause the algorithm to hang when the BAM file has more than 4 billion reads (200x WGS with 150 BP reads).
Bug-fix	Solved issue in QualCal that was slowing down the calculation.
Bug-fix	Solved issue in TNscope® that could report the wrong reference allele for structural variants.
Bug-fix	Solved issue that could cause a job to hang under extremely rare circumstances.
Bug-fix	Solved issue that could cause extra tags in the BAM header to disappear.

Release 201704

Type	Description
Feature	Maintenance update of algorithms.
Feature	Added support for defining a temporary directory, instead of using PWD.
Feature	Added support for type 2 VCF index files.
Feature	Added additional error checks and error reporting.
Feature	Added support for SAC annotation and Allele Specific annotations.
Feature	Added support for additional read filtering: MapQualFilter and OverclippingFilter.
Feature	Added support for CollectVCMetrics.
Feature	Added support for Deduplication equivalent to using BAM files sorted by read name.
Bug-fix	Solved issue in license control that would prevent run when the SENTIEON_AUTH_DATA is of a specific length.
Bug-fix	Solved issue that would not properly parse bed files containing both space and tab delimited fields.
Bug-fix	Solved issue in TNscope® that would report the wrong REF allele for structural variants.
Bug-fix	Solved issue in CoverageMetrics that would produce the wrong summary mean coverage when not using a bed file.

Release 201611.03

Type	Description
Feature	Added support for more options for base quality score recalibration.
Bug-fix	Solved issue in GVCFtyper that could report an incorrect GT or PL when the input GVCFs had been processed with different bed files.
Bug-fix	Solved issue in Realign that caused reads close to the edge of the contig to be realigned beyond the contig boundary.
Bug-fix	Solved issue in Realign that caused a segmentation fault when using known sites VCF including symbolic variants.
Bug-fix	Added support for Realign to update NM and MD tags in the realigned reads.

Release 201611.02

Type	Description
Feature	Added support for calling given known variants to Genotyper, Haplotyper, and TNscope®.
Feature	Added support for outputting physical phasing information of variants in TNhaplotyper and TNscope®.
Feature	Added support for base quality correction in streaming mode in util.
Feature	Maintenance update of HsMetricAlgo.
Feature	Removed redundant nthr argument in VarCal.
Bug-fix	Solved issue in TNscope® causing excessive memory usage in the structural variant calling.
Bug-fix	Solved issue in TNscope® causing a segmentation fault when an output file was not set.
Bug-fix	Solved issue in QualCal in `--plot` mode that was incorrectly reporting the need for known sites.
Bug-fix	Solved incorrect description of filter low_t_alt_frac in TNscope®.

Release 201611.01

Type	Description
Feature	Removed TNscope® temporary files novo_hap.data and novo_sv.data.
Feature	Increased default license timeout from client request.
Bug-fix	Solved an issue causing jobs to hang at the end of the processing when there were issues in the network communication.
Bug-fix	Solved an issue in TNscope® causing an assertion error when pairend reads have inconsistent flags.
Bug-fix	Solved an issue in TNscope® that incorrectly considered reads marked as duplicates in the calculation.

Release 201611

Type	Description
Feature	Added `--emit_mode all` in GVCFtyper.
Feature	Updates to β-version of TNscope®.
Feature	Speed improvement to the alignment and sorting tools.
Feature	Added ContaminationAssessment algorithm for contamination estimation.
Feature	Added detection of truncated VCF input and corrupted cram input files.
Bug-fix	Solved an issue in VarCal that was not producing a plot file when the recalibration failed.
Bug-fix	Solved an issue in VarCal that could cause a segmentation fault when there were not enough licenses for the requested threads.
Bug-fix	Solved an issue in util sort that was causing a segmentation fault when converting an empty sam file to BAM file.

Release 201608.01

Type	Description
Bug-fix	Solved issue in TNseq in tumor-only mode that added to the output VCF an empty column for non-existent NORMAL sample.

Release 201608

Type	Description
Feature	Introduced β-version of new product TNscope® for Tumor-Normal somatic variant calling and structural variant calling.
Feature	Reduced peak memory utilization in klib for alignment.
Feature	Speed improvement in the input file loading of GVCFtyper.
Feature	Speed improvement in the Haplotyper algorithm.
Feature	Made VarCal more robust when building the VQSR gaussian models.
Bug-fix	Cleared up certain error messages to make them more user friendly.
Bug-fix	Solved issue in Genotyper that caused a segmentation fault when using var_type BOTH.

Release 201606.02

Type	Description
Feature	Reduced memory utilization in GVCFtyper to reduce requirements for analysis of large (4000+) cohorts.
Bug-fix	Solved issue in TNsnv that created VCF files non-conforming to the standard.

Release 201606.01

Type	Description
Bug-fix	Solved an issue that prevented licsrvr from serving licenses when the user group list is longer than 1000 characters.

Release 201606

Type	Description
Feature	Maintenance update of TNhaplotyper algorithm (still in β).
Feature	Added support for RNAseq variant calling.
Feature	Added online help.
Feature	Added support for interval padding.
Bug-fix	Solved issue that produced no output in TNhaplotyper when using a PoN or no normal sample data.
Bug-fix	Solved issue preventing BED file with a header from being used.

Release 201603.03

Type	Description
Feature	Added method for inputting long list of VCF files to GVCFtyper.
Feature	Added command line to VCF header.
Feature	Added support for additional annotations on all variant callers.
Bug-fix	Solved issue producing an assertion error when too few variants are called.
Bug-fix	Solved issue reporting the wrong assembly in the VCF header when the FASTA file cannot be interpreted correctly.

Release 201603.02

Type	Description
Bug-fix	Solved issue in TNhaplotyper that incorrectly filtered INDELs.
Bug-fix	Solved issue in TNsnv and TNhaplotyper that made the dbsnp a required argument.
Bug-fix	Solved issue that creates non-conforming VCF files when calling variants in locations where the REF base is M.

Release 201603.01

Type	Description
Feature	Speed improvement in the VQSR algorithm.
Bug-fix	Solved issue that caused VQSR to apply to the wrong type of variants when the variants had a prior LOD annotation.
Bug-fix	Solved issue that slowed down dedup optical duplicate calculation when the number of duplicates at one locus is too large.

Release 201603

Type	Description
Feature	Maintenance update of algorithms.
Feature	Added TNsnv and TNhaplotyper (in β) algorithms for Tumor-Normal and Tumor only somatic variant calling.
Feature	Added support for CRAM files.
Feature	Added support for Haploid and Polyploid samples.
Feature	Added support for setting custom GQ bands for GVCF output.
Bug-fix	Solved issue that dropped reads when the reads extended beyond the contig boundary.

Release 201601.01

Type	Description
Bug-fix	Solved issue in GVCFtyper that produced the wrong variant quality on sites with AAF 0.5 when using more than 50 samples.

Release 201601

Type	Description
Feature	Added support for using interval files only on the realign target creation portion of Realigner.
Bug-fix	Solved issue preventing license server from running in systems with an Infiniband interface.
Bug-fix	Solved issue when merging BAM files that marks reads unmapped when their mate is unmapped.
Bug-fix	Solved issue in Haplotyper in GVCF mode when intervals are used that causes missed variants when the first interval of a contig contains no variants
Bug-fix	Solved issue in GVCFtyper to remove stray/empty SB annotations from the output VCF
Bug-fix	Solved issue causing the corruption of the output VCF under rare conditions involving large number of samples.
Bug-fix	Solved issue that prevented using BAM index files without the optional metadata pseudo bin.

Release 201511.01

Type	Description
Bug-fix	Solved issue in QualCal algorithm that slowed down execution when using BAM files with large number of Readgroups.
Bug-fix	Solved issue in ReadWriter algorithm that produced an incorrect BAM file when using a recalibration table and an input BAM that had PGZ auxiliary data.
Bug-fix	Solved issue in VQSR algorithm that caused the execution to hang when using the results from joint calling of more than 20 samples.

Release 201511

Type	Description
Feature	Maintenance update of algorithms.
Feature	Added pcr_indel_model flag to Haplotyper tool.
Feature	Added phasing information to the output of Haplotyper.
Feature	Added depth metrics tool.
Feature	Added support for compressed VCF/GVCF input and output.
Feature	Added support for Picard style interval files.
Feature	Added wrapper script to remove requirement of LD_LIBRARY_PATH environmental library.
Bug-fix	Added FILTER definition to the VQSR output file header.
Bug-fix	Solved issue that would cause an Out of Memory error in BQSR when using interval files.
Bug-fix	Solved issue that would cause a crash in IndelRealigner when the BAM file has reads with supplementary alignment.

Release 201509

Type	Description
Feature	Reduced resource requirements, including reducing the required maximum number of open files in the system.
Feature	Various improvements in error reporting.
Bug-fix	Solved issue that prevented using multiple BAM files as input to algorithms that produced another BAM file.
Bug-fix	Solved issue that prevented running BQSR when using Readgroups containing spaces.
Bug-fix	Solved issue in Haplotyper that could cause an incorrect variant quality score calculation in low coverage regions. The change could be up to 2% in the quality score, for 1 in 100000 variants.

Release 201508.01

Type	Description
Bug-fix	Solved issue in Realign algorithm that may cause an error when using known sites

Release 201508

Type	Description
Feature	Enhanced error reporting and error handling when dealing with inconsistent input data
Feature	Packaged BWA 0.7.12, and removed non-official options for BWA interface. The results of the packaged BWA are identical to the official BWA
Feature	Grouped the temporary files for VQSR plotting into a single file
Feature	New license server for large clusters
Bug-fix	Solved error in Haplotype Caller when using GVCF emit mode for joint calling
Bug-fix	Solved error in joint calling GVCFtyper that prevented using more than 20 samples

Release 201506

Type	Description
Feature	Added support for Hybrid Selection Analysis metrics
Feature	Unified Genotyper default behavior is to call only SNP variants, to be consistent with GATK 3.3 default behavior
α-Feature	Added initial support for joint variant calling of multiple samples that have ben previously processed individually
Bug-fix	Metrics properly reports unmapped reads when both mates in the pair are unmapped

Release 201505.02

Type	Description
Feature	Speed improvement in Alignment stage
Feature	Speed improvement in Dedup stage
Feature	Added support for temporary BAM files

Release 201505.01

Type	Description
Bug-fix	Issue running VQSR in Mac platform

Release 201505

Type	Description
Feature	Speed improvement via AVX optimization
Feature	Standarized option naming convention
Feature	tmp folder moved to the same location as the job
Feature	Added validation checks to input files
Bug-fix	Solved run to run differences in BQSR when reads have quality scores of 0.
Bug-fix	BQSR applied twice when running variant calling using a recaled BAM file.

Usage changes from previous release

Release 202503.02

This released introduced the following changes in interface and usage:

Added new pgutil tool.
-se_tag option is added in the InsertSizeMetricAlgo to includes single-end consensus reads in the insert size metrics calculation.

Release 202010.04

There are no changes in interface for this release.

Release 202010.03

This released introduced the following changes in interface and usage:

Added new minimap2 tool.
Added new VariantPhaser algorithm for the PacBio® pipeline.

Release 202010.02

This released introduced the following changes in interface and usage:

Added new STAR tool.
Added support in util sort for --trim_primer option to mark primers as soft or hard clips for amplicon samples.

Release 202010.01

This released introduced the following changes in interface and usage:

Added support in TNhaplotyper2 for --given option.
Added support in TNscope® for --trim_primer option to trim primers for amplicon samples.

Release 202010

This released introduced the following changes in interface and usage:

Added 3 new algorithms (ContaminationModel, OrientationBias, and TNfilter) and updated TNhaplotyper2 for TNseq pipelines; in addition, deprecated the tnhapfilter tool, replaced by TNfilter.
Added new option --umi_post_process to util sort for umi pipelines.
Modified the way the tools deal with empty BED interval files: using an empty interval bed file will result in no processing done, as if the interval had 0 length.
The tools now support using VCF files as interval files.
Removed support for the –interval option in the Dedup algo to avoid unintentionally dropping reads from the output file.

Release 201911.01

This released introduced the following changes in interface and usage:

Added suppport in umi extract for 3 input FASTQ files.

Release 201911

This released introduced the following changes in interface and usage:

Added umi extract and umi consensus tools for processing reads containing UMI sequences.
Added --output_flag_filter to ReadWriter to filter reads based on their flags. This option replaces the --read_flag_mask RedWriter option, which has been deprecated.

Release 201808.08

There are no changes in interface for this release.

Release 201808.07

There are no changes in interface for this release.

Release 201808.06

There are no changes in interface for this release.

Release 201808.05

This released introduced the following changes in interface and usage:

Added --genotype_model option in Genotyper, Haplotyer and GVCFtyper algorithm to support new multinomial genotyping model.

Release 201808.03

There are no changes in interface for this release.

Release 201808.02

This released introduced the following changes in interface and usage:

Added TNscope® option –disable_detector to control the type of variants called.
Added support for using multiple –interval options.

Release 201808.01

This released introduced the following changes in interface and usage:

The binaries licsrvr and licclnt require using the bin/sentieon wrapper to be expecuted.

Release 201808

This released introduced the following changes in interface and usage:

Added --bam_output option to TNscope® and TNhaplotyper to output a BAM file including local reassembly of the reads.
Added support for running BWA through the sentieon command wrapper.
Modified plot interface to be consistent with other tools.
Added support for CRAM v3 files.
Added options --snp_heterozygosity and --indel_heterozygosity to Haplotyper and GVCFtyper to input the expected heterozygosity value used to compute prior likelihoods.
Added options --keep_oq and --use_oq to QualCalFilter to keep and use the original qualities when performing BQSR.
Added option --read_flag_mask to ReadWriter to perform customized read filtering.
Added option --replace_rg to driver to modify the RG information of an input BAM file.
Modified the flow for germline variant calling with DNAscope and added DNAModelApply algorithm.

Release 201711.05

There are no changes in interface for this release.

Release 201711.04

There are no changes in interface for this release.

Release 201711.03

This released introduced the following changes in interface and usage:

Introduced multi threaded capability to BWA shm, so that BWA shm accepts the -t NUMBER_THREADS option.
Introduced new environmental variable bwt_max_mem to limit the memory usage of BWA at the expense of speed performance.

Release 201711.02

This released introduced the following changes in interface and usage:

Introduced new QC metrics algorithms: BaseDistributionByCycle, QualityYield, WgsMetricsAlgo, SequenceArtifactMetricsAlgo.
Modified the default for option filter_chimeric_reads in DNAscope when var_type is NOT bnd.

Release 201711.01

This released introduced the following changes in interface and usage:

Added options --version` and ``--dump to licsrvr binary.

Release 201711

This released introduced the following changes in interface and usage:

Added new DNAscope algorithm for germline variant calling and structural variant calling.
Added new TNModelApply algorithm for applying a Machine Learning model to help with variant filtration in TNscope®.
Added new --bam_output option to Haplotyper to output a BAM file including local reassembly of the reads.
Added new option --vqsr_model to ApplyVarCal to allow application of both SNP and INDEL models in a single command line.

Release 201704.03

There are no changes in interface for this release.

Release 201704.02

This released introduced the following changes in interface and usage:

Added --cycle_val_max parameter in QualCal algorithm.
Added --cram_write_options in Dedup, Realigner, ReadWriter, and RNASplitReadsAtJunction algorithms when output format is CRAM.
Removed --min_iter in VarCal algorithm.

Release 201704.01

There are no changes in interface for this release.

Release 201704

This released introduced the following changes in interface and usage:

Added new driver option --temp_dir option to override where the temporary files will be stored.
Added extra annotations for the --annotation option: SAC, AS_BaseQRankSum, AS_FS, AS_InbreedingCoeff, AS_MQRankSum, AS_QD, AS_MQ, AS_ReadPosRankSum, AS_SOR
Added new read filter driver options --read_filter MapQualFilter to filter the input BAM reads by mapping Quality and --read_filter OverclippingFilter to filter the input BAM reads according to their soft clipping characteristics.
Added CollectVCMetrics algorithm to calculate metrics on the VCF output from variant calling.
Added new Dedup options --output_dup_read_name and --dup_read_name to perform dedup to mark both primary and non-primary reads.
Added new options for TNhaplotyper
Added a new ContaminationAssessment option --population to specify the population to represent the baseline allele fraction.

Release 201611.03

This released introduced the following changes in interface and usage:

Added new driver option --read_filter QualCalFilter to perform base quality score recalibration with additional options.

Release 201611.02

This released introduced the following changes in interface and usage:

Introduced --given option in Genotyper, Haplotyper, and TNscope®, to perform calling at given variant sites.
Introduced stream mode in util to perform base quality correction in streaming mode.
Removed --nthr argument from VarCal.
Added extra options to HsMetricAlgo.

Release 201611.01

There are no changes in interface for this release.

Release 201611

This released introduced the following changes in interface and usage:

Introduced ContaminationAssessment algorithm to estimate the contamination in the tumor sample based on the normal variants called.
Added --emit_mode all option in GVCFtyper.

Release 201608.01

There are no changes in interface for this release.

Release 201608

This released introduced the following changes in interface and usage:

Introduced TNscope® algorithm as part of the new TNscope® product for Tumor-Normal somatic variant calling and structural variant calling.

Release 201606.02

There are no changes in interface for this release.

Release 201606.01

There are no changes in interface for this release.

Release 201606

This released introduced the following changes in interface and usage:

Added RNA variant calling tool --algo SplitReadsAtJunction and Haplotyper option --trim_soft_clip to process RNA data aligned using STAR.
Added --help driver option to driver and algorithms to show online help.
Added --interval_padding driver option to pad the input intervals.

Release 201603.03

This released introduced the following changes in interface and usage:

Added --annotation option to Haplotyper and Genotyper to output additional annotations to the result VCF.
Added new method of inputting GVCF files to GVCFtyper.

Release 201603.02

There are no changes in interface for this release.

Release 201603.01

There are no changes in interface for this release.

Release 201603

This released introduced the following changes in interface and usage:

Added TNsnv and TNhaplotyper algorithm for Tumor-Normal and Tumor only somatic variant calling.
Haplotyper and Genotyper have a new optional argument --ploidy to indicate the ploidicity of the sample being processed.
All locations where you can input and output BAM files now accept CRAM files.

Release 201601.01

There are no changes in interface for this release.

Release 201601

This released introduced the following changes in interface and usage:

Realigner has a new optional argument --interval_list to use interval file on the target interval portion of the algorithm, to be in line with Broad’s Best Practice recommendations. Using option --interval in the driver call for realigner would apply the interval to both target creation and realignment, dropping reads in the output BAM file.

Release 201511.01

There are no changes in interface for this release.

Release 201511

This released introduced the following changes in interface and usage:

Haplotyper has a new optional argument --pcr_indel_model to determine the indel model used to weed out false positive indels.
The single interval definition for the --interval driver option is now first-base-1 based as opposed to first-base-0 based. The --interval driver option supports Picard style interval lists.
The driver and util binaries are now accessible through a wrapper script that takes care of setting the LD_LIBRARY_PATH environmental library.
Output VCF files can be produced compressed by using .vcf.gz or .g.vcf.gz extensions.

Release 201509

This release introduced the following changes in interface and usage:

It is no longer necessary to setup a large limit of open files.
In the Remove duplicates stage, the Dedup command now creates an output file reporting the results of the de-duplication.
Added option --bam_compression to all algorithms producing an output BAM file (Dedup, Realign and ReadWriter). The option controls the output BAM file compression level and can be used to achieve a faster speed at the expense of file size.

Release 201508.01

There are no changes in interface for this release.

Release 201508

This release introduced the following changes in interface and usage:

The BWA mapping binary no longer requires or accepts the option -f.
The procedure to generate the plots for base quality score recalibration (BQSR) is now composed of 3 commands instead of 2. Option --pre has been replaced by option --before, and a new option --plot is used to generate the plotting data.
VQSR VarCal algorithm now produces a single file containing all data required to create the VQSR report; this file is specified via the new option --plot_file.

Release 201506

There are no changes in interface for this release.

Release 201505.02

This released introduced the following changes in interface and usage:

In the Alignment stage, the samtools command to convert the output of BWA from SAM to BAM is no longer required, as it is now done in the util command via a new option --sam2bam.
In QualCal algorithm there is a new option --pre RECAL_DATA.TABLE to calculate the data required to create the report.

Release 201505.01

There are no changes in interface for this release.

Release 201505

This release introduced the following changes in interface and usage:

In the GCBias algorithm, the option -s has been replaced by --summary.
In the LocusCollector algorithm, the option -f has been replaced by --fun.
In the Remove duplicates stage, the option -s has been replaced by --score_info.
In the Remove duplicates stage, the option -r has been replaced by --rmdup.
In the BQSR stage, it is no longer necessary to run the varplot command to calculate the data required to create the BQSR report; this call has been merged with the call to apply the recalibration. New option --csv is now used.