Make INDELs parse as INDELs via PyVCF by removing SVTYPE field

remove_svtype.py

#!/usr/bin/env python

import vcf
import sys

'''
PyVCF will parse INDELs as SVs if they have SVTYPE in the INFO field. 
This provides a quick-fix.

contact: adam.ewing@mater.uq.edu.au
'''

def convert(vcf_fn):
    invcf  = vcf.Reader(filename=vcf_fn)
    outvcf = vcf.Writer(sys.stdout, invcf)

    for rec in invcf:
        del(rec.INFO['SVTYPE'])
        outvcf.write_record(rec)

if __name__ == '__main__':
    if len(sys.argv) == 2:
        convert(sys.argv[1])
    else:
        print "usage:",sys.argv[0],"<VCF>"