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davidaknowles/make_het.sh

Created June 17, 2022 17:28
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Make a dummy vcf with all SNPs being heterozygous for one individual. SOME_SAMPLE needs to be set to one of the sample names in the input.vcf.
Raw
make_het.sh
#!/bin/bash
bcftools view -H input.vcf.gz | \
awk '{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $5 "\t" $6 "\t" $7 "\t" $8 "\t" $9 "\t" "0/1"}' | \
cat <(bcftools view -h -s SOME_SAMPLE input.vcf.gz) - | \
bgzip > \
output.vcf.gz
bcftools view -H output.vcf.gz | awk '{ print $1 "\t" $2 - 1 "\t" $2 }' | bgzip > output.bed.gz
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