Vcf Edit !!top!!

You have a list of positions to remove (BED file). Perform a to exclude them:

sed -E 's/(TEL.*:)([0-9])/\1+1\2/g' contacts.vcf > new.vcf vcf edit

reader = vcf.Reader(open('input.vcf', 'r')) reader.filters['LowDepth'] = vcf.parser.Filter('LowDepth', 'Depth below threshold') reader.infos['OriginalDP'] = vcf.parser.Info('OriginalDP', 1, 'Integer', 'Original DP value') You have a list of positions to remove (BED file)