From b73d72fe94d0cf5512eb342d53026e6a9d6f72d6 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Sun, 6 Jan 2013 01:56:57 -0500 Subject: [PATCH] update docs for LEftAlignVariants --- .../sting/gatk/walkers/variantutils/LeftAlignVariants.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java index fbb81fda0..16a9125a5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java @@ -54,9 +54,10 @@ import java.util.*; * Left-aligns indels from a variants file. * *

- * LeftAlignVariants is a tool that takes a VCF file and left-aligns any indels inside it. The same indel can often be + * LeftAlignVariants is a tool that takes a VCF file and left-aligns the indels inside it. The same indel can often be * placed at multiple positions and still represent the same haplotype. While the standard convention with VCF is to * place an indel at the left-most position this doesn't always happen, so this tool can be used to left-align them. + * Note that this tool cannot handle anything other than bi-allelic, simple indels. Complex events are written out unchanged. * *

Input

*