Python VCF.get_header_type Examples

Example #1

    for key, value in genotype_dict.items():
        if value == "HET":
            het_list.append(key)
        if value == "ALT_HOM":
            hom_list.append(key)

    return het_list, hom_list


vcf = VCF(vcf_file)

samples = vcf.samples

tot_alleles = 2 * len(samples)

CSQ_description = vcf.get_header_type(key="CSQ").get("Description")
CSQ_format = CSQ_description.split("Format: ")[-1]
CSQ_keys = CSQ_format.split("|")

print(vcf.raw_header, end="")

for record in vcf:

    svlen = record.INFO.get("SVLEN")
    if svlen is None:
        svlen = record.INFO["END"] - record.POS

    genotypes = parse_genotype(record, samples)
    het_list, hom_list = get_alt_samples(genotypes)

    num_alleles = len(het_list) + 2 * len(hom_list)