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YaqingLiu 5 년 전
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1개의 변경된 파일3개의 추가작업 그리고 6개의 파일을 삭제
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    -6
      tasks/bcftools.wdl

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bcftools view ${pon_vcf1} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf1).gz bcftools view ${pon_vcf1} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf1).gz
bcftools index /cromwell_root/tmp/bcftools/$(basename $pon_vcf1).gz

bcftools view ${pon_vcf2} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf2).gz bcftools view ${pon_vcf2} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf2).gz
bcftools index /cromwell_root/tmp/bcftools/$(basename $pon_vcf2).gz

bcftools view ${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf3).gz bcftools view ${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf3).gz
bcftools index /cromwell_root/tmp/bcftools/$(basename $pon_vcf3).gz
bcftools index /cromwell_root/tmp/bcftools/*.vcf.gz


bcftools merge -m all -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz |\ bcftools merge -m all -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz |\
bcftools plugin fill-AN-AC |\ bcftools plugin fill-AN-AC |\
bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf
else else
touch panel_of_normal.vcf touch panel_of_normal.vcf
fi fi

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