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hall-lab / svtools

Tools for processing and analyzing structural variants.
MIT License
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Svtyper, svtyper-sso and svtools genetype output discrepant genotypes #293

Open yachenhu opened 5 years ago

yachenhu commented 5 years ago

Hi,

I have run svtype, svtyper-sso and svtools genotype on the same dataset. I found the variants with GT of ./. had discrepant values in other genotype fields.

svtools genotype: GT ./. svtyper-sso: GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB ./.:.:.:.:0:0:0:0:0:0:0:0:0:0:. svtyper: GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB ./.:.:.:-1344,-435,-2711:4252:3522:729:3522:729:3522:729:0:0:0:0.17

It shows that only the svtyper has a valid output, while it spent a dramatically long time to calculate it, says 10-20 folds than the other two.

I wonder what happened here and should I just ignore those strange variants?

Thanks, Yachen