split gtex genotype file by chromosome number

Question

[rheab1230]

Hello, I am trying to submit a job in michigan imputation server to get imputed dosage for gtex genotype file. But when I submit it says there are more than one chromosome and cannot submit job for imputation. Does anyone know how should I split gtex genotype file by chromosome number. I tried to use plink software but getting error. The command used:

for chr in $(seq 1 22); do plink --file /Databases/GTEx/downloaded/dbGAP/GTEx_Analysis_Indiv_VEP_annot.vcf.gz \ --chr $chr \ --recode \ --out myGwasData.chr$chr ; done

the error:

128869 MB RAM detected; reserving 64434 MB for main workspace.
Error: Failed to open
/scratch/Databases/GTEx/downloaded/dbGAP/GTEx_Analysis_Indiv_VEP_annot.vcf.gz.map.
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 myGwasData.chr6.log.
Options in effect:
  --chr 6
  --file /scratch/Databases/GTEx/downloaded/dbGAP/GTEx_Analysis_Indiv_VEP_annot.vcf.gz
  --out myGwasData.chr6
  --recode

Does anyone know how to solve this.

Answer 1

[Pierre Lindenbaum]

I'm not a plink expert but shouldn't you use the option --vcf ? https://www.cog-genomics.org/plink/1.9/input

--vcf loads a (possibly gzipped) VCF file, extracting information which can be represented by the PLINK 1 binary format and ignoring everything else (after applying the load filters described below). For example, phase and dosage information are currently discarded. (This situation will improve in the future, but we do not have plans to try to handle everything in the file.)

[rheab1230]

yes --vcf should be used instead of --file