Plink related questions

[Lucas]

How do you convert MyHeritage raw data to PLINK format? It looks like this:

$ head -n20 MyHeritage_raw_dna_data.csv
##fileformat=MyHeritage
##format=MHv1.0
##chip=GSA
##timestamp=2021-09-23 08:59:54 UTC
##reference=build37
#
# MyHeritage DNA raw data.
# For each SNP, we provide the identifier, chromosome number, base pair position and genotype.
# The genotype is reported on the forward (+) strand with respect to the human reference build 37.
# THIS INFORMATION IS FOR YOUR PERSONAL USE AND IS INTENDED FOR GENEALOGICAL RESEARCH
# ONLY. IT IS NOT INTENDED FOR MEDICAL OR HEALTH PURPOSES. PLEASE BE AWARE THAT THE
# DOWNLOADED DATA WILL NO LONGER BE PROTECTED BY OUR SECURITY MEASURES.
RSID,CHROMOSOME,POSITION,RESULT
"rs547237130","1","72526","AA"
"rs562180473","1","565703","AA"
"rs575203260","1","567693","TT"
"rs3131972","1","752721","GG"
"rs200599638","1","752918","GG"
"rs12184325","1","754105","CC"
"rs114525117","1","759036","GG"

If you have problem with those company formats, you can alwas can use DNAKitStudio for convertion to 23me format for example.

[Komintasavalta]

If you have problem with those company formats, you can alwas can use DNAKitStudio for convertion to 23me format for example.

I don't have a Windows VM, so I registered an account at dnagenics.com and used the option "DNA Tools > RAW Converter".

But apparently the 23andme format is the same as the MyHeritage format, except it doesn't have a header line and it's TSV and not CSV. So you can just do this:

plink --23file <(grep -v ^\# MyHeritage_raw_dna_data.csv|sed 1d|tr , \\t|tr -d \") --make-bed --out mybed