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mhguo1 / TRAPD

Burden testing against public controls
MIT License
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MAF and AF #7

Open sureyana956 opened 5 years ago

sureyana956 commented 5 years ago

Hi, thanks for providing this tool. I have a question regarding how MAF cutoff was applied to subset SNP lists. Is alt always considered as the minor allele in your scripts? Take rs7954255 for example, Latino and African actually have a AF greater than 0.5, which means the reference allele becomes the minor allele. Did you take that into consideration in your count_controls.py and make_snp_file.py scripts?

mhguo1 commented 5 years ago

Hi, The code currently only considers the alternate allele as the minor allele. It is a good point and I will try to revise TRAPD to take the minor allele rather than alternate allele. It may be tricky in certain situations (especially if the minor allele is different across populations).

Thanks, Mike

On Jun 6, 2019, at 7:18 PM, sureyana956 notifications@github.com wrote:

Hi, thanks for providing this tool. I have a question regarding how MAF cutoff was applied to subset SNP lists. Is alt always considered as the minor allele in your scripts? Take rs7954255 for example, Latino and African actually have a AF greater than 0.5, which means the reference allele becomes the minor allele. Did you take that into consideration in your count_controls.py and make_snp_file.py scripts?

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