From 45717349dce9f26fa865807c269fa47a1651b997 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Wed, 10 Oct 2012 16:01:37 -0400 Subject: [PATCH] Fixing BQSR bug reported on the forum for reads that begin with insertions. --- .../sting/gatk/walkers/bqsr/BaseRecalibrator.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index 49bfc6e06..f61fdda60 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -225,7 +225,7 @@ public class BaseRecalibrator extends LocusWalker implements TreeRed final GATKSAMRecord read = p.getRead(); final int offset = p.getOffset(); - if (readHasBeenSkipped(read) || isLowQualityBase(p)) // This read has been marked to be skipped or base is low quality (we don't recalibrate low quality bases) + if (readHasBeenSkipped(read) || p.isInsertionAtBeginningOfRead() || isLowQualityBase(p) ) // This read has been marked to be skipped or base is low quality (we don't recalibrate low quality bases) continue; if (readNotSeen(read)) {