Sentieon software for DNA pipeline analysis

2016-04-29
Release 201603.02
Bug-Fix: Solved issue in TNhaplotyper that was incorrectly filtering INDELs.
Bug-Fix: Solved issue in TNsnv and TNhaplotyper that was making 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 was causing VQSR to apply to the wrong type of variants when the variants had a prior LOD annotation.
Bug-Fix: Solved issue that was slowing 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 was dropping 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 was 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
