Calculate Jukes-Cantor, Kimura, Tamura-Nei etc distances from BAM files · Biostar

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Calculate Jukes-Cantor, Kimura, Tamura-Nei etc distances from BAM files

Hi,

Does anyone know if there's an existing tool to calculate genetic distances between query and subject sequences in BAMs/SAMs? I'm reasonably sure it's possible to identify transitions and transversions using data from the MD flag and the sequence, and from that calculate genetic distance, however I don't know if I'll need to write my own tool or if one already exists.

Cheers, James.

kimura minimap2 samtools biopython pysam

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written 2.7 years ago by James G •

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