Question: How to recode VCF from bed bim and fam files in plink with filter?
gravatar for DN93
22 months ago by
DN930 wrote:

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.

linux snp plink bim vcf • 1.2k views
ADD COMMENTlink modified 22 months ago • written 22 months ago by DN930
gravatar for chrchang523
22 months ago by
United States
chrchang5237.6k wrote:
  1. Can you post more of the .log file; at minimum, include the first line which has the version/date?
  2. "Failed to open <filename>" probably means that the filename you provided doesn't exist (which may be because of a typo or a wrong directory). If it just says "Failed to open" without a filename, that's very weird, but I can't say more unless you provide the plink version/date.
ADD COMMENTlink written 22 months ago by chrchang5237.6k

Thank you for your reply. I am using Plink 1.9 from 15 August 2017. I also forgot to mention I am using a limited amount of ram, would this potentially be the cause? And if so do I need to specifiy my variants to filter by before trying to open this files as then I guess it would only search for and take the relevant variants from the file?

ADD REPLYlink modified 22 months ago • written 22 months ago by DN930

Try rerunning this with a more recent plink 1.9 build.

If this fails, double- and triple-check that all your filenames are actually correct. Nothing else you mentioned is relevant. I won’t respond further here unless you provide not only the new .log output, but also the appropriate “ls” command verifying that the files are all there.

ADD REPLYlink modified 22 months ago • written 22 months ago by chrchang5237.6k
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