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natsuhiko / rasqual

Robust Allele Specific Quantification and quality controL
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Minor allele frequency filtering #25

Closed kwcurrin closed 5 years ago

kwcurrin commented 5 years ago

Hello,

For minor allele frequency filtering with -a/--minor-allele-frequency, does RASQUAL calculate the minor allele frequency or just take it from the VCF info file? I have some VCF files where I have removed a few individuals, so the MAF in the info field is not correct for the new set of samples. If RASQUAL takes MAF from info, then I will need to make a new set of VCFs when subsetting samples.

Thanks!

Kevin

kwcurrin commented 5 years ago

Sory, I meant "info field" of VCF, not "info file"

natsuhiko commented 5 years ago

Hi Kevin,

RASQUAL directory calculates MAF from genotype dosage and doesn't use INFO field.

Best regards, Natsuhiko

kwcurrin commented 5 years ago

Great! Thanks!