why some variants are filtered out in the final output?
Opened this issue · 4 comments
fengpku commented
my input number of variants is 1096103, but the output is only 189948 lines. Is that correct?
Thanks!
FerRacimo commented
Dear fengpku,
GRoSS automatically filters out variants with global minor allele frequency
< 5%, or that contain missing data. Could this apply in your case?
Cheers,
Fernando
…On Fri, Oct 16, 2020 at 6:01 AM fengpku ***@***.***> wrote:
my input number of variants is 1096103, but the output is only 189948
lines. Is that correct?
Thanks!
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fengpku commented
Thank you for your reply. I think you are correct, the MAF<0.5 variants are filtered out.
Cheers.
Yuanqing
fengpku commented
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
FerRacimo commented
Yes, sorry, it's 1%.
…On Mon, Feb 22, 2021 at 8:16 PM fengpku ***@***.***> wrote:
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
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Fernando Racimo, PhD
Associate Professor of Population Genetics
Globe Institute
University of Copenhagen
Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark