From a4a41458efc3b3745356b0ddc89fceee4cef2137 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 1 Aug 2012 10:33:41 -0400 Subject: [PATCH] Update docs of FastaAlternateReferenceMaker as promised in older GS thread --- .../sting/gatk/walkers/fasta/FastaAlternateReference.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java index 92549b821..28cfdd5cd 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java @@ -47,7 +47,8 @@ import java.util.List; *

* Given variant tracks, it replaces the reference bases at variation sites with the bases supplied by the ROD(s). * Additionally, allows for one or more "snpmask" VCFs to set overlapping bases to 'N'. - * Note that if there are multiple variants at a site, it takes the first one seen. + * Note that if there are multiple variants at a site, it chooses one of them randomly. + * Also note that this tool works only for SNPs and for simple indels (but not for things like complex substitutions). * Reference bases for each interval will be output as a separate fasta sequence (named numerically in order). * *

Input