Sentieon software for DNA pipeline analysis

2017-08-17
Release 201704.02
Bug-Fix: Solved issue in TNhaplotyper in --detect_pon that produces a non-compliant VCF.
Bug-Fix: Solved issue in TNscope in --given mode that was not reporting records on areas of 0 depth coverage.
Bug-Fix: Solved issue in CoverageMetrics reporting wrong cumulative_coverage_counts, coverage.statistics when input bam has multipe different read groups.
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 Realigner when input bam file has wrong MC tag type.
Bug-Fix: Solved issue in QualCal where cycle_val_max parameter was not opened to user.

2017-06-10
Release 201704.01
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.

2017-05-12
Release 201704
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.

2017-03-15
Release 201611.03
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.

2017-01-31
Release 201611.02
Feature: Added support for calling given known variants in 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 utilization 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.
Bug-Fix: Solved issue in Realign that may set the incorrect bin to the unmapped reads of a mapped/unmapped pair that got its positions adjusted close to a bin boundary.

2016-12-16
Release 201611.01
Feature: Removed TNscope temporary files novo_hap.data and novo_sv.data.
Feature: Increased default license timeout from client request.
Bug-Fix: Solved issue causing jobs to hang at the end of the processing when there were issues in the network communication.
Bug-Fix: Solved issue in TNscope causing an assertion error when pairend reads have inconsistent flags. 
Bug-Fix: Solved issue in TNscope that incorrectly considered reads marked as duplicates in the calculation.

2016-11-20
Release 201611
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 issue in VarCal that was not producing a plot file when the recalibration failed.
Bug-Fix: Solved issue in VarCal that could cause a segmentation fault when there were not enough licenses for the requested threads.
Bug-Fix: Solved issue in util sort that was causing a segmentation fault when converting an empty sam file to bam file.

2016-09-17
Release 201608.01
Bug-Fix: Solved issue in TNseq in tumor-only mode that added to the output VCF an empty column for non-existent NORMAL sample.

2016-08-31
Release 201608
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.
Feature: 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.

2016-07-25
Release 201606.02
Feature: Reduced memory utilization in GVCFtyper to reduce requirements for analyss of large (4000+) cohorts.
Bug-Fix: Solved issue in TNsnv that created VCF files non-conforming to the standard.
 
2016-07-15
Release 201606.01
Bug-Fix: Solved issue that prevented licsrvr from serving licenses when the user group list is longer than 1000 characters.

2016-06-31
Release 201606
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.

2016-05-31
Release 201603.03
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.

2016-04-29
Release 201603.02
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.

2016-03-25
Release 201603.01
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.

2016-03-11
Release 201603
Feature: Maintenance update of algorithms.
Feature: Added TNseq-snv algorithm for Tumor-Normal and Tumor only somatic variant calling.
Feature: Added support for CRAM files.
Feature: Added support for Haploid and Polyploid samples.
Bug-Fix: Solved issue that droped reads when the reads extended beyond the contig boundary.

2016-02-12
Release 201601.01
Bug-Fix: Solved issue in GVCFtyper that produced the wrong variant quality on sites with AAF > 0.5 when using more than 50 samples.

2016-01-31
Release 201601
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 as 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.

2015-12-17
Release 2015011.01
Bug-Fix: Solved issue in QualCal algorithm that slowed down execution when using bam files with large number of Read Groups.
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.

2015-11-30
Release 201511
Feature: Maintenance update of algorithms.
Feature: Added depth metrics tool.
Feature: Added pcr_indel_model flag to Haplotyper tool.
Feature: Added phasing information to the output of Haplotyper.
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.

2015-09-20
Release 201509
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 Read Groups 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.

2015-09-02
Release 201508.01
Bug-Fix: Solved issue in Realign algorithm that may cause an error when using known sites.

2015-08-31
Release 201508
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 0.7.12
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

2015-06-30
Release 201506
Feature: Added Hybrid Selection Analysis metrics
Feature: Unified Genotyper default behavior is to call only SNP variants, to be consistent with GATK 3.3 default behavior 
Bug-Fix: Alignment metrics properly reports unmapped reads when both mates in the pair are unmapped
Alpha-Feature: Added initial support for joint variant calling of multiple samples that have ben previously processed individually

2015-06-15
Release 201505.02
Feature: Speed improvement in Alignment stage
Feature: Speed improvement in Dedup stage
Feature: Added support for temporary bam files

2015-06-09
Release 201505.01
Bug-Fix: Issue running VQSR in Mac platform

2015-05-31
Release 201505
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


2015-03-02
1. add vqsr
2. support IONTORRENT platform

2015-01-16

1. Bring the code to be compatible with GATK 3.3

2. Add support for different variant emit modes:
        --emit_mode=variant     Emit confident variants only (default)
        --emit_mode=confident   Emit confident variants or reference
        --emit_mode=all         Emit all sites
   Applicable to both Genotyper and Haplotyper.

3. Add the ability to generate graphical(pdf) outputs for various reports:
     o  metrics
        - MeanQualityByCycle
        - QualDistribution
        - GCBias
     o  BQSR

2014-12-18

1, Add command line options to set calling or emitting confidence thresholds:
        --algo Genotyper --emit_conf=10 --call_conf=30
   Applicable to both Genotyper and Haplotyper.

2, Add command line option to set minimum pruning factor in local assembly:
        --algo Haplotyper --prune_factor=3
   Applicable to Haplotyper.

3, Add command line option to set chromosome region filters:
        driver -c /path/to/filter.bed
   This is a driver level option, therefore applicable to algos.

4, Generate additional variant annotations. Here's the full list,
        AC, AF, AN, DP, MLEAC, MLEAF, MQ, MQ0, QD, FS,
        BaseQRankSum, ClippingRankSum, MQRankSum, ReadPosRankSum
