-ploidy 1 still has diploid genotypes

hsinnan75 / MapCaller

MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes

MIT License

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-ploidy 1 still has diploid genotypes #30

Closed tseemann closed 4 years ago

tseemann commented 4 years ago

When I use -ploidy 1 I would expect GT=0 or GT=1 only, but I get GT=1|1

PASS DP=18;AD=18;DUP=0;AF=1.000;GT=1|1;TYPE=SUBSTITUTE

hsinnan75 commented 4 years ago

Hi, I made a mistake on labeling genotypes. I'd like to know what the genotype label will be in such case (GT=0 or GT=1). Thank you!

tseemann commented 4 years ago

and for -ploidy 4 you would have GT=1|1|1|1 etc. (i think)

hsinnan75 commented 4 years ago

Thank you! I've updated MapCaller (v0.9.9.15) to fix the wrong annotation. However, MapCaller supports monoploid and diploid for now. I have to survey how to deal with annotation for triploid and more.

tseemann commented 4 years ago

Thank you.