PLINK not converting entire vcf to bed file
0
0
Entering edit mode
18 months ago

here is my code :

[ethan.kreuzer@hydra1 2_Population_stratification]$ plink --vcf ALL.2of4intersection.20100804.genotypes.vcf.gz --make-bed --out ALL.2of4intersection.20100804.genotypes
[mii] Please select a module to run plink:
       MODULE                 PARENT(S)
    1  plink/1.9b_6.21-x86_64 StdEnv/2020
    2  plink/1.07             nixpkgs/16.09 intel/2018.3
    3  plink/1.9b_5.2-x86_64  nixpkgs/16.09
    4  plink/1.9b_4.1-x86_64  nixpkgs/16.09
Make a selection (1-4, q aborts) [1]: 1
[mii] loading StdEnv/2020 plink/1.9b_6.21-x86_64 ...
PLINK v1.90b6.21 64-bit (19 Oct 2020)          www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to ALL.2of4intersection.20100804.genotypes.log.
Options in effect:
  --make-bed
  --out ALL.2of4intersection.20100804.genotypes
  --vcf ALL.2of4intersection.20100804.genotypes.vcf.gz

50289 MB RAM detected; reserving 25144 MB for main workspace.
--vcf: 32k variants complete.
Error: File read failure.
[ethan.kreuzer@hydra1 2_Population_stratification]$ ls
1_Main_script_QC_GWAS.txt                    ALL.2of4intersection.20100804.genotypes-temporary.bed  ALL.2of4intersection.20100804.genotypes.vcf.gz  HapMap_3_r3_12.fam  MDS_merged.R  plink.fam
2_Main_script_MDS.txt                        ALL.2of4intersection.20100804.genotypes-temporary.bim  HapMap_3_r3_12.bed                              HapMap_3_r3_12.log  plink.bed     plink.log
ALL.2of4intersection.20100804.genotypes.log  ALL.2of4intersection.20100804.genotypes-temporary.fam  HapMap_3_r3_12.bim                              indepSNP.prune.in   plink.bim

Can someone help me understand how to convert the entire document vcf.gz file? Thank you

tutorial from : "https://github.com/MareesAT/GWA_tutorial/tree/master" in the "2_Population_stratification.zip" section

vcf plink genome1000 bed • 972 views
ADD COMMENT
0
Entering edit mode

Error: File read failure.

Verify that your VCF file is readable all the way through and not corrupt/incomplete.

ADD REPLY
0
Entering edit mode

do you know how I could investigate this? I'm not sure what I should be looking for. Thank you for your reply.

ADD REPLY
0
Entering edit mode

I realize that it's not preinstalled on your system, but plink 2.0 provides a more useful error message here, and is generally a much better choice than plink 1.x for working with VCF data.

ADD REPLY

Login before adding your answer.

Traffic: 1940 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6