call variants DV/LS on chrY contigs

marschall-lab / project-male-assembly

HGSVC SIG: targeted chromsome Y assembly

MIT License

8 stars 1 forks source link

call variants DV/LS on chrY contigs #7

Closed ptrebert closed 2 years ago

ptrebert commented 2 years ago

identify clusters of HET variants as potential misassembled regions

ptrebert commented 2 years ago

this has been implemented and tested for the first handful of samples. so far, looks like we get <100 HET SNPs per assembly (irrespective of population of origin) for HiFi with Qual >= 10 For ONT/HG00358, no variant left after filtering, more test samples still running...

pilleh commented 2 years ago

@ptrebert Sorry, forgot to reply to this. Sounds pretty good! I bet there is clustering of these SNPs to specific regions. Based on HiFi depth there are some collapses in some samples, at least some are probably located in those regions as well.