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darencard/missing_from_vcf.md

Last active January 12, 2017 16:26
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Extract the proportion of missing data per sample in a VCF/BCF file
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missing_from_vcf.md

Simply replace <<FILE>> with your properly formated VCF/BCF file name (2 places). Required bcftools v. 1.2+.

paste \
<(bcftools query -f '[%SAMPLE\t]\n' <<FILE>> | head -1 | tr '\t' '\n') \
<(bcftools query -f '[%GT\t]\n' <<FILE>> | awk -v OFS="\t" '{for (i=1;i<=NF;i++) if ($i == "./.") sum[i]+=1 } END {for (i in sum) print i, sum[i] / NR }' | sort -k1,1n | cut -f 2)
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