Tuesday, November 1, 2011

prepare dbsnp132

1.
awk '/^chrM/ {print $0}' ../res/hg19/dbsnp_132.hg19.vcf > m.vcf
awk '/^chrM/ {next} {print $0}' ../res/hg19/dbsnp_132.hg19.vcf > wom.vcf
cat m.vcf >> wom.vcf
rm m.vcf
mv wom.vcf hg19.dbsnp_132.vcf

2.
vim hg19.dbsnp_132.vcf
delete all non-mapped contigs in header section ##contig

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