From cb284eebde82268960c123ba3726a91b4089a034 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Tue, 29 Nov 2011 14:00:57 -0500 Subject: [PATCH] Further updating VQSR tutorial wiki docs to reflect the bundle --- .../gatk/walkers/variantrecalibration/ApplyRecalibration.java | 2 +- .../gatk/walkers/variantrecalibration/VariantRecalibrator.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java index af7e6e991..62fbad4b9 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java @@ -76,7 +76,7 @@ import java.util.*; * java -Xmx3g -jar GenomeAnalysisTK.jar \ * -T ApplyRecalibration \ * -R reference/human_g1k_v37.fasta \ - * -input NA12878.HiSeq.WGS.bwa.cleaned.raw.b37.subset.vcf \ + * -input NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf \ * --ts_filter_level 99.0 \ * -tranchesFile path/to/output.tranches \ * -recalFile path/to/output.recal \ diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java index 21e96b4a1..520393898 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java @@ -92,7 +92,7 @@ import java.util.*; * java -Xmx4g -jar GenomeAnalysisTK.jar \ * -T VariantRecalibrator \ * -R reference/human_g1k_v37.fasta \ - * -input NA12878.HiSeq.WGS.bwa.cleaned.raw.b37.subset.vcf \ + * -input NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf \ * -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf \ * -resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.sites.vcf \ * -resource:dbsnp,known=true,training=false,truth=false,prior=8.0 dbsnp_132.b37.vcf \