I am trying to create a vcf in plink. Currently as a practice run I have tried this with just looking at chromosome 1 and I have a snpids.txt file with 10 snp ids to filter by :
plink --bed /data/chr1.bed --bim /data/chr1.bim --fam /data/chr1.fam --recode vcf-iid --out new_vcf.vcf --keep-fam /data/chr1.fam --extract /data/snpids.txt --write-snplist
However this goes on to give:
192580 MB RAM detected; reserving 86290 MB for main workspace. 1065753 variants loaded from .bim file. Error: Failed to open
I assume this means I am not successfully fitlering these files before recoding into a vcf? I am very new to using plink, is it possible I am just ordering the code wrongly? Any guidance would be appreciated.