Tutorial

Querying VCF file

Using del2 (bottom) as example, query the COSMIC VCF database:

import pysam
from variantpost import Variant

reference = pysam.FastaFile("/path/to/GRCh38.fa")
cosmic = pysam.VariantFile("/path/to/cosmic.v89.vcf(.gz)")

# del2
v = Variant("17", 31224665, "CC", "C", reference)

Normalization query (default) returns VCF entries that are identical after normalization:

norm_hits = v.query_vcf(cosmic) # list of 2 hit VCF entries (del1 and del2)

for hit in norm_hits:
    print(hit["INFO"]["CNT"])

    #COSMIC count for del1
    #COSMIC count for del2

Locus query returns VCF entries located at the normalized genomic locus:

locus_hits = v.query_vcf(cosmic, matchby="locus") # list of 5 hit VCF entries (all indels)

for hit in locus_hits:
    print(hit["INFO"]["CNT"])

    #COSMIC count for del1
    ...
    #COSMIC count for ins3

Exact query only returns a VCF entry matching without normalization:

exact_hit = v.query(cosmic, matchby="exact") # list of a hit VCF entry (del2)

print(exact_hit[0]["INFO"]["CNT"])

#COSMIC count for del2

Phasing to complex variant