VCF to BED

= VCF to BED = datadir="/ngs/hg19/GATK-hg19" for i in `cat ../cases.list` do filename="${i}.hg19.snps.PASS.vcf" sed -e 's/chr//' ${datadir}/$filename | awk '{OFS="\t"; if (!/^#/){print "chr"$1,$2-1,$2,$4"/"$5,"+"}}'  \ >  hg19-bed/GATK-hg19/${i}.hg19.snps.bed done

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