export-allele to get the genotype counts for variants specified in the export allele file

[SN]

Hi Christopher,

I am using the following command :

plink --bfile data --chr $chr --from-bp "$start" --to-bp "$end" --keep "$ids" --maf 0.01 --export A --export-allele "path" --out "$plink_out"

THe region that I am extracting has 4195 variants. My export-allelle text file has 3330 variants out 4195 for which I want to create the genotype matrix. However, the output raw file that I get contains all 4195 variants. How can get only 3300 variants that I specify in my export-allele file ?  

Thanks

PLINK v2.00a2LM 64-bit Intel (6 Mar 2019)      www.cog-genomics.org/plink/2.0/

(C) 2005-2019 Shaun Purcell, Christopher Chang   GNU General Public License v3

Logging to /gpfs/pace2/project/coc-ideas/shared/snagpal3/GEXP_Imputation_PROTECT/PROTECT_TRAINING/Gene_Subset_Plink/ENSG00000211895_IGHA1_chr14.log.

Options in effect:

  --bfile /gpfs/pace2/project/coc-ideas/shared/snagpal3/GEXP_Imputation_PROTECT/PROTECT_TRAINING/Gene_Subset_Plink/ENSG00000211895_IGHA1_chr14

  --export A

  --export-allele /gpfs/pace1/project/bio-gibson/snagpal3/Projects/IBD/GEXP_Imputation_PROTECT/PROTECT_EXPORT_ALT_ALLELE.txt

  --out /gpfs/pace2/project/coc-ideas/shared/snagpal3/GEXP_Imputation_PROTECT/PROTECT_TRAINING/Gene_Subset_Plink/ENSG00000211895_IGHA1_chr14

Start time: Tue Apr 23 10:52:18 2019

129084 MiB RAM detected; reserving 64542 MiB for main workspace.

Using up to 12 threads (change this with --threads).

331 samples (161 females, 170 males; 331 founders) loaded from

/gpfs/pace2/project/coc-ideas/shared/snagpal3/GEXP_Imputation_PROTECT/PROTECT_TRAINING/Gene_Subset_Plink/ENSG00000211895_IGHA1_chr14.fam.

4195 variants loaded from

/gpfs/pace2/project/coc-ideas/shared/snagpal3/GEXP_Imputation_PROTECT/PROTECT_TRAINING/Gene_Subset_Plink/ENSG00000211895_IGHA1_chr14.bim.

1 binary phenotype loaded (331 cases, 0 controls).

--export-allele: 3330 variants updated, 6236660 variant IDs not present.

--export A pass 1/1: writing... done.

--export A:

/gpfs/pace2/project/coc-ideas/shared/snagpal3/GEXP_Imputation_PROTECT/PROTECT_TRAINING/Gene_Subset_Plink/ENSG00000211895_IGHA1_chr14.raw

written.

[Christopher Chang]

Adding “—extract <export-allele file>” to your command line will probably work.

[SN]

Thanks! It worked!