Release notes and usage changes
Updates from previous releases
Release 202503.03
Type |
Description |
|---|---|
Feature |
Introduced β-version of germline structure variant calling and copy number variation calling in the Sentieon Pangenome pipeline. |
Feature |
Introduced β-version of deduplication and consensus read generation for single end DNA data. |
Bug-fix |
Solved issue in GeneEditEvaluator algorithm that produced incorrect p-values. |
Bug-fix |
Solved issue in bwa mem that could cause an assertion on ARM based CPUs. |
Bug-fix |
Solved an issue in TNhaplotyper2 in sharded mode that lost variants under very rare circumstances when output format is compressed VCF. |
Other |
Sentieon BAM/CRAM output header @HD VN is updated to 1.6. |
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 |
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 |
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 |
Bug-fix |
Solved issue in SequenceArtifactMetricsAlgo that would cause an error when the |
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 |
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 |
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 |
Bug-fix |
Solved issue in Realigner when input BAM file has wrong MC tag type. |
Bug-fix |
Solved issue in TNhaplotyper in |
Bug-fix |
Solved issue in TNscope® in |
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 |
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 |
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. |