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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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Support for ploidy != 2 #22

Closed tseemann closed 4 years ago

tseemann commented 4 years ago

Genotypes seem to be called as diploid n=2. Is MapCaller a naive frequency caller or does it have a statistica model? I was wondering if you would support different ploidy? I am interested in n=1 (haploid, bacteria). Or should I just filter the VCF ?

hsinnan75 commented 4 years ago

Basically, MapCaller is based on allele frequency to call variants. It supports haploid and diploid. I think it should be able to support different ploidy. I'll try with some synthetic data sets.

hsinnan75 commented 4 years ago

I added a new argument (-ploidy) for specifying the number of complete sets of chromosomes in a cell. If your sample is monoploid, you may use run MapCaller with "-ploidy 1". Please let me know if you find any problems on running MapCaller. Thank you!

tseemann commented 4 years ago

Could you please tag a release for it?

git tag v0.9.9.8 && git push --tags

hsinnan75 commented 4 years ago

Sure, the current version is v0.9.9.9. There is one more step for v1.0.0.0 which will include CNV detection.

tseemann commented 4 years ago

New related bug #30