plink2 to convert phased WGS vcf (for use with snpnet)

[Charleen Adams]

Hello, 

I have a phased WGS vcf. I've tried to use plink2 to convert it to pgen, pvar.zst, and psam files in order to run snpnet. It's not generating a pvar.zst file, though. (And when I try to run snpnet, the error I get is "Can't rename columns that don't exist. Column "#FID" doesn't exist.") 

Can plink2 convert phased WGS vcf files? Would I need to manipulate my WGS vcf in some way in order to get the pvar.zst file as well? 

Any thoughts and directions would be greatly appreciated. 

Best, 

Charleen 

Here is the log file: 

PLINK v2.00a3LM AVX2 Intel (14 May 2022)
Options in effect:
  --make-pgen
  --out /n/messerlian_lab/Users/cdadams/binary_fileset
  --vcf phased.vcf.gz

Hostname: holy7c12610.rc.fas.harvard.edu
Working directory: /net/holy-nfsisilon/ifs/rc_labs/messerlian_lab/Users/cdadams/
Start time: Thu Nov 17 23:27:36 2022

Random number seed: 1668745656
192926 MiB RAM detected; reserving 96463 MiB for main workspace.
Allocated 72347 MiB successfully, after larger attempt(s) failed.
Using up to 48 threads (change this with --threads).
--vcf: 48446031 variants scanned.
--vcf:
/n/messerlian_lab/Users/cdadams/binary_fileset-temporary.pgen
+
/n/messerlian_lab/Users/cdadams/binary_fileset-temporary.pvar.zst
+
/n/messerlian_lab/Users/cdadams/binary_fileset-temporary.psam
written.
809 samples (0 females, 0 males, 809 ambiguous; 809 founders) loaded from
/n/messerlian_lab/Users/cdadams/binary_fileset-temporary.psam.
48446031 variants loaded from
/n/messerlian_lab/Users/cdadams/binary_fileset-temporary.pvar.zst.
Note: No phenotype data present.
Writing
/n/messerlian_lab/Users/cdadams/binary_fileset.psam
... done.
Writing
/n/messerlian_lab/Users/cdadams/binary_fileset.pvar
... done.
Writing
/n/messerlian_lab/Users/cdadams/binary_fileset.pgen
... done.

End time: Thu Nov 17 23:40:59 2022

[Christopher Chang]

Use "--make-pgen vzs" instead of plain --make-pgen to generate a compressed .pvar file.

Yes, plink2 is able to preserve phase information.