gatk-3.8/public/java/src/org/broadinstitute/sting
Mark DePristo 6df96644d9 Unified, standard IndelSummary metrics for VariantEval
-- Now you always get SNP and indel metrics with VariantEval!
--   Includes Number of SNPs, Number of singleton SNPs, Number of Indels, Number of singleton Indels, Percent of indel sites that are multi-allelic, SNP to indel ratio, Singleton SNP to indel ratio, Indel novelty rate, 1 to 2 bp indel ratio, 1 to 3 bp indel ratio, 2 to 3 bp indel ratio, 1 and 2 to 3 bp indel ratio, Frameshift percent, Insertion to deletion ratio, Insertion to deletion ratio for 1 bp events, Number of indels in protein-coding regions labeled as frameshift, Number of indels in protein-coding regions not labeled as frameshift, Het to hom ratio for SNPs, Het to hom ratio for indels, a Histogram of indel lengths, Number of large (>10 bp) deletions, Number of large (>10 bp) insertions, Ratio of large (>10 bp) insertions to deletions
-- Updated VE integration tests as appropriate
2012-03-22 21:24:37 -04:00
..
alignment At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings. 2012-01-17 14:47:53 -05:00
analyzecovariates Active Region Traversal should use GATKSAMRecords everywhere instead of SAMRecords. misc cleanup. 2012-02-03 17:13:52 -05:00
commandline Merged bug fix from Stable into Unstable 2012-02-27 17:13:17 -05:00
gatk Unified, standard IndelSummary metrics for VariantEval 2012-03-22 21:24:37 -04:00
jna Device files like /dev/null are now tracked as special by Queue and are not used to generate .out file paths, scattered into a temporary directory, gathered, deleted, etc. 2012-01-23 16:17:04 -05:00
queue Device files like /dev/null are now tracked as special by Queue and are not used to generate .out file paths, scattered into a temporary directory, gathered, deleted, etc. 2012-01-23 16:17:04 -05:00
utils Caching log calculations cut the non-Map runtime of HaplotypeCaller in half. Moved the qual log cache used in HC and PairHMM into a common place and added unit tests. 2012-03-21 08:45:42 -04:00