Confused about PED and MAP file

Question

[Begonia_pavonina]

Hello everyone,

I try to use an R package called detectRUNS, and the documentation suggest I have to use "the Plink ped and map files" to run it. https://cran.r-project.org/web/packages/detectRUNS/vignettes/detectRUNS.vignette.html#importing-data-from-external-files

However, consulting the PLINK documentation, it seems that the ped and map files are input for PLINK, and not an output. https://zzz.bwh.harvard.edu/plink/data.shtml

I am very confused about these files, and wonder if it is possible to create them from a VCF file for example?

Thanks for your help!

Answer 1

[4galaxy77]

.ped and .map files can be used as both the input and output from plink (although the formats are quite out of date now and shouldn't be used unless necessary, like this case).

You can create a .vcf file from a .ped and .map by running the following command in plink

plink --vcf myvcf.vcf --recode --out myplink

[Begonia_pavonina]

Thank you for the answer, and for the warning about the aging .ped and .map formats.

I have been able to generate .ped and .map files from a .vcf file with your script. Thanks again!