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Published 20 hours ago • verified publisher icon francois-a

how fastqtl deal with ./. genotype

Open zhangpicb opened this issue 2 years ago • 2 comments

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!

zhangpicb avatar Sep 18 '22 14:09 zhangpicb

Hi, missing genotypes are imputed to the mean, see here. FYI, an improved QTL mapper is available: tensorQTL.

francois-a avatar Sep 19 '22 00:09 francois-a

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!

zhangpicb avatar Dec 04 '22 09:12 zhangpicb