From 1749a490421b386938a8cd599ff39a75f92667a5 Mon Sep 17 00:00:00 2001 From: chartl Date: Fri, 7 May 2010 18:08:13 +0000 Subject: [PATCH] Mapping and base quality thresholds for DoC default to none git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3326 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/coverage/DepthOfCoverageWalker.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java index ad58553c6..5968ab815 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java @@ -82,9 +82,9 @@ public class DepthOfCoverageWalker extends LocusWalker, Covera @Argument(fullName = "nBins", doc = "Number of bins to use for granular binning", required = false) int nBins = 499; @Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum mapping quality of reads to count towards depth. Defaults to 50.", required = false) - byte minMappingQuality = 50; + byte minMappingQuality = -1; @Argument(fullName = "minBaseQuality", shortName = "mbq", doc = "Minimum quality of bases to count towards depth. Defaults to 20.", required = false) - byte minBaseQuality = 20; + byte minBaseQuality = -1; @Argument(fullName = "printBaseCounts", shortName = "baseCounts", doc = "Will add base counts to per-locus output.", required = false) boolean printBaseCounts = false; @Argument(fullName = "omitLocusTable", shortName = "omitLocusTable", doc = "Will not calculate the per-sample per-depth counts of loci, which should result in speedup", required = false)