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EichlerLab / pav

Phased assembly variant caller
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Can PAV works in high het organisms? #51

Closed ghost closed 3 months ago

ghost commented 1 year ago

Hello,

My organism has a heterozygosity of a few percents, so we see a snp every 30 bases. Since the human genome has a snp every 1000 bases, I was wondering if PAV has expectations regarding high het. Will it penalizes variants because because they are too close to one another?

Thanks

paudano commented 1 year ago

PAV does not assume any model of variation, so it should work well as long as the assembly alignments work. By default, it uses minimap parameter -x asm20 (with other parameters), which assumes 5% divergence from the reference. The default options might work (SNP every 30 bp is 3% divergence), but parameters can be adjusted if needed.