wbgalvao/fix-multianno-header.sh

Created August 13, 2020 18:10

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Given a multianno file (annovar's output) fix its header by adding the vcf columns (CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT and SAMPLE)

Raw

fix-multianno-header.sh

	#!/bin/bash

	multianno=${1}

	header=$(head -1 ${multianno})
	fixedHeader=$(echo "${header}" \
	\| sed 's/Otherinfo/VCF_CHROM/' \
	\| awk '{print $0"\tVCF_POS\tVCF_ID\tVCF_REF\tVCF_ALT\tVCF_QUAL\tVCF_FILTER\tVCF_INFO\tVCF_FORMAT\tVCF_SAMPLE"}' \
	)

	sed -i '1 s,'"${header}"','"${fixedHeader}"',' ${multianno}

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