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Entering edit mode
6.5 years ago

Hello to you all!

I want to ask if somebody was able to import gVCF files into plink. The thing is that in order to answer a specific question I need the gVCF file since I need information of both polymorphic and monomorphic sites. So if I transform the gVCF file into a normal VCF one (to be used by plink) I will lose information for the purpose of my analysis.

I have been trying to find around the internet some tutorial or reference regarding this issue but all what I have found is how to import normal VCF files (which is pretty straightforward). I did not find anything regarding gVCF files.

Thanks for your time and help people!

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Entering edit mode

It is indeed a good question.

I have successfully produced a .hom file with the following script, but unfortunately the number of runs drop drastically compared to a single-sample plink analysis. I think the software search for Runs Of Homozygosity common to all the samples included in the gVCF file. I am not sure yet how to prevent it.

plink --vcf GVCF_SNPs_edit.vcf --homozyg --out GVCF_SNPs  --allow-extra-chr --no-parents --no-sex --no-pheno  --homozyg-window-snp 50 --homozyg-snp 50 --homozyg-window-missing 3 --homozyg-kb 100 --homozyg-density 1000

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Entering edit mode

Why no answer here? This sounds like a good question.