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7.7 years ago
w0nderingatwork
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40
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
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)
Dear Ahill, thanks a lot. We will try it that way. Cheers.
Hi Ahil, How can I compare genotypes in two ped files?
Regards, Tarek