From ebcd333ed8c918251b6378eb15ae39da2a2561fd Mon Sep 17 00:00:00 2001 From: carneiro Date: Wed, 18 May 2011 20:08:39 +0000 Subject: [PATCH] Quick small updates: SelectVariants: typo MethodsDevelopmentPipeline: Added CEU Trio WGS dataset git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5818 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/variantutils/SelectVariants.java | 2 +- scala/qscript/core/MethodsDevelopmentCallingPipeline.scala | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index 7bcf33dec..b023f5a8c 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -92,7 +92,7 @@ public class SelectVariants extends RodWalker { @Argument(fullName="selectSNPs", shortName="snps", doc="Select only SNPs.", required=false) private boolean SELECT_SNPS = false; - @Argument(fullName="selectIndels", shortName="indels", doc="Select only SNPs.", required=false) + @Argument(fullName="selectIndels", shortName="indels", doc="Select only Indels.", required=false) private boolean SELECT_INDELS = false; diff --git a/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala b/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala index 47741deb1..5367ef7fe 100755 --- a/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala +++ b/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala @@ -129,6 +129,10 @@ class MethodsDevelopmentCallingPipeline extends QScript { new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.bwa.cleaned.recal.bam"), new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, 97.0, !lowPass), + "WGSTrio" -> new Target("CEUTrio.WEx", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37, + new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.bwa.cleaned.recal.bam"), + new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** + "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, 99.0, !lowPass), "FIN" -> new Target("FIN", b37, dbSNP_b37, hapmap_b37, indelMask_b37, new File("/humgen/1kg/processing/pipeline_test_bams/FIN.79sample.Nov2010.chr20.bam"), new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **