Closed steveners closed 7 years ago
Hi Stevener,
I suggest to remove all homozygous SNVs. Specifically, the SNVs with extreme frequencies. The MI distribution is also affected by the homozygous SNVs. Thanks.
Best, Qing
2017-06-20 14:00 GMT-07:00 steveners notifications@github.com:
Hello! I have some question: in previous issues you reccomend to remove homozygous SNV's from SNV list. Now I have a question: should I remove homozygous SNV's or I should remove homozygous SNP's known from dbSNP? I found in article that this requirement is necessary only for GLM stage: you train this model assuming that all SNP's from list are heterozygous. So why should I remove all homozygous SNV's? Thank you!
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Hi Qing,
Thank you! It is just strange that there is no information about it in paper.
Hello! I have some question: in previous issues you reccomend to remove homozygous SNV's from SNV list. Now I have a question: should I remove homozygous SNV's or I should remove homozygous SNP's known from dbSNP? I found in article that this requirement is necessary only for GLM stage: you train this model assuming that all SNP's from list are heterozygous. So why should I remove all homozygous SNV's? Thank you!