1000G Phase 3 GRCh38 liftover - EUR-nonFIN subset

Question

[gokberk]

Hi everyone,

I ran plink on 1000G phase 3 GRCh38 genotype files and merged bed, bim and fam files of all chromosomes. Now, I need to subset these files based on EUR participant IDs in 1KG phase 3 data. Here is the command I will use:

plink  --bfile /data/1KG_phase3/GRCh38/plink/1KG_phase3_GRCh38_allchr \
         --keep /data/1KG_phase3/GRCh38/plink/eur_subsets/1KG_phase3_European_samples.txt \
         --make-bed \
         --out /data/1KG_phase3/GRCh38/plink/eur_subsets/1KG_phase3_GRCh38_EUR_allchr

However, I was wondering where/how to get the 1KG_phase3_European_samples.txt file, which should include 1KG Phase 3 EUR-nonFIN FamilyIDs and IndividualIDs based on this post.

Thanks a lot!

Answer 1

[gokberk]

Got it, extracted non-Finnish EUR individuals' IDs from this list.

[999.me]

Hi, How did you merge the bed/bim/fam files ? I am trying to do the same but I get an error that says ".fam files cannot be read". Can you please share your commands ?

Thank you!