Bioinformatics with Python Cookbook - Second Edition

How to do it...

Take a look at the following steps:

1. Let's start by inspecting the information that we can get per record:

import vcfv = vcf.Reader(filename='genotypes.vcf.gz')print('Variant Level information')infos = v.infosfor info in infos:    print(info)print('Sample Level information')fmts = v.formatsfor fmt in fmts:    print(fmt)

We start by inspecting the annotations that are available for each record (remember that each record encodes a variant, such as SNP, CNV, INDELs, and so on, and the state of that variant per sample). At the variant (record) level, we find AC: the total number of ALT alleles in called genotypes, AF: the estimated allele frequency, NS: the number of samples with data, AN: the total number of alleles in called genotypes, ...