Release notes and usage changes¶
Updates from previous releases¶
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 202010.02¶
This released introduced the following changes in interface and usage:
- Added new STAR tool.
- Added support in util sort for
--trim_primeroption 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
--givenoption. - Added support in TNscope® for
--trim_primeroption 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_processto 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 extractfor 3 input FASTQ files.
Release 201911¶
This released introduced the following changes in interface and usage:
- Added
umi extractandumi consensustools for processing reads containing UMI sequences. - Added
--output_flag_filterto ReadWriter to filter reads based on their flags. This option replaces the--read_flag_maskRedWriter 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_modeloption 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_outputoption 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_heterozygosityand--indel_heterozygosityto Haplotyper and GVCFtyper to input the expected heterozygosity value used to compute prior likelihoods. - Added options
--keep_oqand--use_oqto QualCalFilter to keep and use the original qualities when performing BQSR. - Added option
--read_flag_maskto ReadWriter to perform customized read filtering. - Added option
--replace_rgto 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 ``--dumpto 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_outputoption to Haplotyper to output a BAM file including local reassembly of the reads. - Added new option
--vqsr_modelto 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_maxparameter in QualCal algorithm. - Added
--cram_write_optionsin Dedup, Realigner, ReadWriter, and RNASplitReadsAtJunction algorithms when output format is CRAM. - Removed
--min_iterin 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_diroption to override where the temporary files will be stored. - Added extra annotations for the
--annotationoption: 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 MapQualFilterto filter the input BAM reads by mapping Quality and--read_filter OverclippingFilterto 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_nameand--dup_read_nameto perform dedup to mark both primary and non-primary reads. - Added new options for TNhaplotyper
- Added a new ContaminationAssessment option
--populationto 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 QualCalFilterto perform base quality score recalibration with additional options.
Release 201611.02¶
This released introduced the following changes in interface and usage:
- Introduced
--givenoption 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
--nthrargument 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 alloption 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 SplitReadsAtJunctionand Haplotyper option--trim_soft_clipto process RNA data aligned using STAR. - Added
--helpdriver option to driver and algorithms to show online help. - Added
--interval_paddingdriver option to pad the input intervals.
Release 201603.03¶
This released introduced the following changes in interface and usage:
- Added
--annotationoption 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
--ploidyto 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_listto use interval file on the target interval portion of the algorithm, to be in line with Broad’s Best Practice recommendations. Using option--intervalin 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_modelto determine the indel model used to weed out false positive indels. - The single interval definition for the
--intervaldriver option is now first-base-1 based as opposed to first-base-0 based. The--intervaldriver 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_compressionto 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
--prehas been replaced by option--before, and a new option--plotis 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
--preRECAL_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
--csvis now used.