File: vcf2bed.py

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libvcflib 1.0.0~rc2%2Bdfsg-2
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#!/usr/bin/env python

import sys

for line in sys.stdin:
    if line.startswith('#'):
        continue
    fields = line.strip().split()
    # VCF is 1-based, BED is 0-based half open
    # print out chrom, start, end, 
    chrom = fields[0]
    start = int(fields[1]) - 1
    span = len(fields[3]) # handle multi-base alleles
    end = start + span
    name = fields[2]
    print "\t".join(map(str, [chrom, start, end, name]))