PyVCF example using Cython and BGZIP compressed output

filter_vcf.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-

import sys
import os
import cyvcf
import Bio.bgzf


vcf_input = sys.argv[1]
vcf_name = os.path.basename(vcf_input).split(".gz")[0]
bgzip_output = Bio.bgzf.BgzfWriter(filename="{0}.filtered.gz".format(vcf_name))

vcf_reader = cyvcf.Reader(filename=(vcf_input))
vcf_writer = cyvcf.Writer(bgzip_output,vcf_reader)

for record in vcf_reader:

        if record.call_rate <= 0.95:
                continue

        if not record.is_snp:
                continue

        if record.num_het / float(len(record.samples)) > 0.02:
                continue

        samples_cov = filter(lambda x: x["DP"] >= 8,record.samples)
        if len(samples_cov) / float(len(record.samples)) <= 0.5:
                continue

        genotypes = map(lambda x: x.gt_type, record.samples)

        print "Coord: {0} {1} {2}: {3}".format(record.CHROM,record.POS,genotypes,(record.num_hom_alt*2 + record.num_het) / float((len(record.samples)-record.num_unknown)*2))
        if (record.num_hom_alt*2 + record.num_het) / float((len(record.samples)-record.num_unknown)*2) < 0.05:
                continue

        if record.QUAL < 30:
                continue


        vcf_writer.write_record(record)


vcf_output.close()