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abyzovlab / CNVpytor

a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads
MIT License
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haploid genome error #204

Closed cfz1998 closed 8 months ago

cfz1998 commented 8 months ago

All chromosome types were specified as "S" for my reference genome.

image

I still got Heterozygote. What's the problem?

image

arpanda commented 8 months ago

Many cnvpytor functions are hardcoded assuming the gnome is diploid. The VCF output is one of those functions. It appears that the snapshot in question is derived from the VCF output of the call.

Please manually inspect the Manhattan plot and calls if its make sense or not to proceed for the analysis.

-Arijit