How to use the cyvcf2.VCFReader function in cyvcf2
To help you get started, we’ve selected a few cyvcf2 examples, based on popular ways it is used in public projects.
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AndersenLab / VCF-kit / vcfkit / utils / primer_vcf.py View on Github 
def fetch_variant_count(self, region, sample_set = None):
"""
Fetches variant count in a region.
"""
v = VCFReader(self.filename)
sample_indices = [v.samples.index(x) for x in sample_set]
vc = 0
for i in v(self.region):
gt_len = len(set([i.gt_types[x] for x in sample_indices]))
if gt_len > 1:
vc += 1
return vcdef _get_vcf_reader(self):
return vcf.VCFReader(self.args.vcf)
