FerRacimo/GRoSS

why some variants are filtered out in the final output?

Opened this issue · 4 comments

my input number of variants is 1096103, but the output is only 189948 lines. Is that correct?
Thanks!

Thank you for your reply. I think you are correct, the MAF<0.5 variants are filtered out.
Cheers.
Yuanqing

Hi Fernando,
I see in the LoadFiles.R line 37 : fcutoff <- 0.01. I think this should be the filter threshold.
So is the MAF cutoff 0.01 or 0.05?
Thanks,
Yuanqing