Limited support for SNV/MNVs

For single- and multi-nucleotide variants (SNV/MNVs), Variant object is fully supported. VariantAlignment object supports naive allele counting.

_images/mnv.svg

“Naive” counting only includes aligned events

import pysam
from indelpost import Variant, VariantAlignment

reference = pysam.FastaFile("/path/to/reference.fa")
bam = pysam.AlignmentFile("/path/to/example.bam")

v = Variant("chrN", 5, "GTC", "TAG", reference)
valn = VariantAlignment(v, bam)

cnt = valn.count_alleles()
print(cnt)
#(3, 2) the soft-clipped read (bottom) not included as target