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Compare genotypes from sequencing (vcf) and microarrays (ped)

Dear all, we have sequencing data in vcf format as well as genotype array data in ped format for our samples. For reasons of quality control, we'd like to compare the genotypes from both experiments. Which is the best way to do that? Is there a way to compare both filetypes in Plink/Seq? Thanks and kind regards

sequencing snp vcf ped
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written by w0nderingatwork • w0nderingatwork

You could use plink --vcf --recode to convert .vcf to .ped/.map (see here), and then compare .peds. Obviously this assumes variants are identified the same way your input .vcf and .ped files. Imagine you would want to filter to variants that are present in both your input sets, which could be accomplished by using plink filtering options (here)

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written by Ahill Ahill

Dear Ahill, thanks a lot. We will try it that way. Cheers.

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written by w0nderingatwork • w0nderingatwork

Hi Ahil, How can I compare genotypes in two ped files?

Regards, Tarek

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written by tarek.mohamed tarek.mohamed

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