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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
public Unified, standard IndelSummary metrics for VariantEval 2012-03-22 21:24:37 -04:00
settings Rev. tribble to fix BED codec bug in tribble 51 2012-01-17 16:40:26 -05:00
.gitignore Minor additions to the shared .gitignore file, now that Mark has checked one in. 2011-10-26 12:24:28 -04:00
LICENSE One last test... 2011-06-28 19:18:17 -04:00
build.xml Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
ivy.xml S3 upload now directly creates the XML report in memory and puts that in S3 2012-01-29 15:14:58 -05:00