A little script to expand VCF to allow the key-value list to be easily sorted/filtered

expandvcf.py

import sys
from copy import copy

used_keys = ['DP', 'AF1', 'CI95', 'DP4', 'MQ', 'PV4', 'INDEL']
initial_dict = dict([(k, '') for k in used_keys])

for ln in sys.stdin:
    d = copy(initial_dict)

    cols = ln.rstrip().split("\t")

    #print cols[7]
    for keypair in cols[7].split(';'):
        if '=' in keypair:
           key, val = keypair.split("=")
           d[key] = val
        else:
           d[keypair] = keypair

    cols.extend([d[key] for key in used_keys])
    print "\t".join(cols)