VCF to PGEN with split chromosome

[Anthony Marcketta]

Hi Chris,

Has the handling of split chromosomes in VCF files changed in recent builds? This command used to work to convert VCF to PGEN while sorting the variants, I believe the last build I tested was the Oct 20 2020 build.

plink2 \

--vcf input.vcf.gz \

--make-pgen \

--double-id \

--allow-extra-chr \

--output-chr 26 \

--sort-vars \

--indiv-sort n \

--out intermediate

PLINK v2.00a3LM 64-bit Intel (2 Mar 2021)      www.cog-genomics.org/plink/2.0/

(C) 2005-2021 Shaun Purcell, Christopher Chang   GNU General Public License v3

Logging to intermediate.log.

Options in effect:

  --allow-extra-chr

  --double-id

  --indiv-sort n

  --make-pgen

  --memory 100000000000

  --out intermediate

  --output-chr 26

  --sort-vars

  --vcf input.vcf.gz

Start time: Tue Mar 23 19:45:07 2021

31149 MiB RAM detected; reserving 100000000000 MiB for main workspace.

Allocated 23890 MiB successfully, after larger attempt(s) failed.

Using up to 16 threads (change this with --threads).

--vcf: 65k variants converted.   

--vcf: 131k variants converted.

--vcf: 196k variants converted.

--vcf: 262k variants converted.

--vcf: 327k variants converted.

--vcf: intermediate-temporary.pgen + intermediate-temporary.pvar.zst +

intermediate-temporary.psam written.

18270 samples (0 females, 0 males, 18270 ambiguous; 18270 founders) loaded from

intermediate-temporary.psam.

Error: intermediate-temporary.pvar.zst has a split chromosome. Use --make-pgen

+ --sort-vars to remedy this.

End time: Tue Mar 23 19:46:16 2021

I am using --make-pgen and --sort-vars.

Thanks for your help,

Tony

[Christopher Chang]

Not intentionally, it looks like I broke the regular --sort-vars use case in the process of making --pmerge-list respect the flag.  Fixing now.