Mark DePristo dc4932f93d VariantEval module to stratify the variants by whether they overlap an interval set ... The primary use of this stratification is to provide a mechanism to divide asssessment of a call set up by whether a variant overlaps an interval or not. I use this to differentiate between variants occurring in CCDS exons vs. those in non-coding regions, in the 1000G call set, using a command line that looks like: -T VariantEval -R human_g1k_v37.fasta -eval 1000G.vcf -stratIntervals:BED ccds.bed -ST IntervalStratification Note that the overlap algorithm properly handles symbolic alleles with an INFO field END value. In order to safely use this module you should provide entire contigs worth of variants, and let the interval strat decide overlap, as opposed to using -L which will not properly work with symbolic variants. Minor improvements to create() interval in GenomeLocParser.		2011-11-10 10:58:40 -05:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	VariantEval module to stratify the variants by whether they overlap an interval set	2011-11-10 10:58:40 -05:00
test	Moving unclaimed walker with bad integration test to archive	2011-11-07 13:16:38 -05:00