From d6992d12632c0cfc6b3bdf5b88872fb2d4625e41 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 23 Sep 2013 15:48:47 -0400 Subject: [PATCH] Updated docs to tell users not to use PCR indel error modeling for PCR free data. --- .../sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java | 1 + 1 file changed, 1 insertion(+) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java index 8776a5e4b..360d0979f 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java @@ -475,6 +475,7 @@ public class HaplotypeCaller extends ActiveRegionWalker, In /** * Which PCR indel error model should we use when calculating likelihoods? If NONE is selected, then the default base * insertion/deletion qualities will be used (or taken from the read if generated through the BaseRecalibrator). + * VERY IMPORTANT: when using PCR-free sequencing data we definitely recommend setting this argument to NONE. */ @Advanced @Argument(fullName = "pcr_indel_model", shortName = "pcrModel", doc = "The PCR indel model to use", required = false)