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how fastqtl deal with ./. genotype #23

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zhangpicb opened this issue Sep 18, 2022 · 2 comments
Open

how fastqtl deal with ./. genotype #23

zhangpicb opened this issue Sep 18, 2022 · 2 comments

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@zhangpicb
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Hi @francois-a

Thanks for your beautiful code!

I have a question about fastqtl.
How fastqtl deal with ./. genotype?fastqtl impute this site or using other methods to deal ./. genotype?If fastqtl impute this site,how to get the output of impute result .

Thanks in advanced!
@francois-a
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Hi, missing genotypes are imputed to the mean, see here. FYI, an improved QTL mapper is available: tensorQTL.

@zhangpicb
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Hi @francois-a

Thanks very much for your quick reply!

How to get GTEx v8 same imputated vcf ?or where to download imputated GTEx v8 vcf, because GTEx_v8 Freeze.SHAPEIT2_phased.vcf.gz still have missing genotypes

Thanks in advanced!

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@francois-a @zhangpicb