Release notes for GATK version 3.7

GATK 3.7 was released on December 12, 2016. Itemized changes are listed below. For more details, see the user-friendly version highlights.

39da22b - Changes to use the median rather than the second best likelihood for the NON_REF allele
a8797f2 - Fixed merging of GVCF blocks by fixing rounding of GQ values in ReferenceConfidenceModel
ce4ed1f - Remove NON_REF from allSites VCF output
ba21b22 - Do not emit GVCF block definitions in the header of the final VCF emitted by GenotypeGVCFs
6670d12 - Changed maximum allowed GQB value to 100
e7bd143 - Added exception for GQB values greater than MAX_GENOTYPE_QUAL and tests
9ae9b26 - Deprecate -stand_emit_conf
04a70bb - Remove -stand_emit_conf argument
5b8bf1c - Change default value of STANDARD_CONFIDENCE_FOR_CALLING to 10
a8db074 - Backport new AFCalculator
ad3e4f4 - Backport numerics changes in new qual
dc0fa3f - Fixes NaN issue in new Qual calculator

d7f1a9c - Lots of small improvements to Mutect2 code
408d31d - More small refactorings of Mutect2 code
ff1e3a3 - Finish porting MuTect1 clustered read position filter
ce7d4bd - Port the strand bias filter from M1 and refactored code around SomaticGenotypingEngine; added a new integration test
1350c0e - Add new annotator for M1 clustered read position filter and M1 strand bias filter
095a469 - Cleaned up SomaticGenotypingEngine::callMutations and added some TODOs
e6d0318 - Expose downsampling arguments in Mutect

a557ff3 - RCM Variant sites merger won't output PL when there are too many alleles in order to avoid memory issues with large cohort runs
7296dbf - Remove alt alleles, when genotype count is explosively large, based on alleles' highest supporting haplotype score; max tolerable genotype count is controlled by a default value overridable by user
5b09639 - Impose a maximum allele list message length
7cd8a66 - Make sure that multi-allelic uninformative PLs (0,0,...,0) stay uninformative after biallelization
f182fc1 - Make alt allele removal by likelihoods robust to ref allele indices
1709765 - Fixed a max priority Q error while removing alt alleles when faced with high ploidy and allele count

69af359 - Added option to merge GenomeLocs that are abutting (contiguous) rather than actually overlapping
541243b - Make interval padding work for "exclude intervals"
4e4ac94 - Enable control of reporting periodicity
68f1822 - Set HTSJDK log level
359f078 - Throw an exception if the BQSR input covariates file is not found

975c17a - Throw an exception for invalid Picard intervals
ce1d4c8 - Upgrade Apache Commons Collections to version 3.2.2
355d053 - Move htsjdk and picard to version 2.5.0
08b8eab - Move htsjdk to ver 2.6.1 and picard to ver 2.6.0
4d45102 - Move htsjdk to ver 2.8.1 and picard to ver 2.7.2
f410451 - Change HashMap to LinkedHashMap for predictable ordering
5fac5c8 - Added support for directly reading SRA runs
a5cc81a - Remove SRA group
899453b - Write saved WARN messages to stderr instead of stdout
bed804d - Replace SAMFileReader with calls to SamReaderFactory
a48d36d - Assign correct ambiguity code for * allele
496564f - Removed spanning deletions if the deletion was removed when subsetting
a37886f - Fix adapter boundary for positive strand in handling of overlapping read pairs
f6b18c8 - Fix issue where VCF files with "bcf" in the name were output to BCF
4d6d207 - Replace VariantContextWriterFactory with VariantContextWriterBuilder
6b8740e - Make exit system file type message generic

e6d34af - Make ReadPosRankSumTest.isUsableRead() account for deletions
e4786ed - Added regression test for genotyping of spanning deletions in GenotypeGCVFs
f709898 - Add integration test using -maxNumPLValues for GenotypeGVCFs
dfcec64 - Fix BetaTestingAnnotation group Add test
f7ff6b8 - Change a truth VCF in VQSR tests
d5ad2f0 - Make getElementForRead() in RankSumTest robust