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1 parent cd90dc4 commit 1eede50Copy full SHA for 1eede50
wdl/CleanVcf1.wdl
@@ -1360,7 +1360,7 @@ task CleanVcf1_23 {
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command <<<
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set -euxo pipefail
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cat <(zcat ~{cleanmale_vcf}|egrep "##") \
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- <(paste <(zcat ~{cleanmale_vcf}|egrep -v "##") <(zcat ~{cleanfemale_vcf}|cut -f10-|egrep -v "##") <(zcat ~{cleanother_vcf}|cut -f10-|egrep -v "##") ) \å
+ <(paste <(zcat ~{cleanmale_vcf}|egrep -v "##") <(zcat ~{cleanfemale_vcf}|cut -f10-|egrep -v "##") <(zcat ~{cleanother_vcf}|cut -f10-|egrep -v "##") ) \
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|bgzip \
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>combinedsex.vcf.gz
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tabix -p vcf combinedsex.vcf.gz
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