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Plink ped format

Heys,

I was trying to convert a vcf to a ped file format. However, when my samples had a genotype 0/0, it did not appear as 0 in my ped file. I am just obtaining 1 or 2 and the 0 are missing. This is the code I am using:

plink --bfile leopard1 --recode12 --out leopard1 --allow-extra-chr

I am using Plink v1.9

Thanks in advance!

plink
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written by gubrins gubrins

1 answer

You included the flag --recode12. The plink doc says --recode12 "will recode the alleles as 1 and 2 (and the missing genotype will always be 0)." Missing genotypes generally appear as ./. in a vcf and they would be coded as 0 0 (missing) in the ped file with the --recode12 flag. 0/0 would not appear as 0's in the ped file with the flags you included. Might recommend you check out the plink documentation for more on the recode flag.

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written by caleb_dume • caleb_dume

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