From d276ec59ce0b6d9de1a47bc2034bc866cff734a8 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 26 Sep 2019 18:49:35 -0500
Subject: [PATCH] add filter cnvkit
---
variants/cnvkit.sh | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/variants/cnvkit.sh b/variants/cnvkit.sh
index 1898189..1031ec3 100755
--- a/variants/cnvkit.sh
+++ b/variants/cnvkit.sh
@@ -61,8 +61,8 @@ cnvkit.py coverage ${sbam} ${targets}targets.bed -o ${pair_id}.targetcoverage.cn
cnvkit.py coverage ${sbam} ${targets}antitargets.bed -o ${pair_id}.antitargetcoverage.cnn
cnvkit.py fix ${pair_id}.targetcoverage.cnn ${pair_id}.antitargetcoverage.cnn ${normals} -o ${pair_id}.cnr
cnvkit.py segment ${pair_id}.cnr -o ${pair_id}.cns
-cnvkit.py call ${pair_id}.cns -o ${pair_id}.call.cns
-#cnvkit.py call ${pair_id}.cns -v common_variants.vcf -o ${pair_id}.ballelecall.cns
+cnvkit.py call --filter cn ${pair_id}.cns -o ${pair_id}.call.cns
+#cnvkit.py call --filter cn ${pair_id}.cns -v common_variants.vcf -o ${pair_id}.ballelecall.cns
cnvkit.py scatter ${pair_id}.cnr -s ${pair_id}.call.cns -t --segment-color "blue" -o ${pair_id}.cnv.scatter.pdf
cut -f 1,2,3 ${pair_id}.call.cns | grep -v chrom | bedtools intersect -wao -b /project/shared/bicf_workflow_ref/human/GRCh38/cytoBand.txt -a stdin |cut -f 1,2,3,7 > ${pair_id}.cytoband.bed
perl $baseDir/filter_cnvkit.pl ${pair_id}.call.cns
--
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