why some variants are filtered out in the final output?

[fengpku]

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

[FerRacimo]

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

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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! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABLXSAVIIOTBNAG5V43KJNLSK7ARZANCNFSM4SSZ3A6Q> .

-- Fernando Racimo, PhD Associate Professor of Population Genetics Globe Institute University of Copenhagen Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark

[fengpku]

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

[fengpku]

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]

Yes, sorry, it's 1%.

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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 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABLXSAT6IRTX6572PHSTEDLTAKUQVANCNFSM4SSZ3A6Q> .

-- Fernando Racimo, PhD Associate Professor of Population Genetics Globe Institute University of Copenhagen Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark