the number of variants in the pvar and pgen do not match

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Jingjing Bai

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May 17, 2022, 5:58:29 AM5/17/22

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Hi ,

I am removing the duplicate variants in the subset-pruned_data but got the following errors. Can you please help me to solve that?

PLINK v2.00a3LM 64-bit Intel (10 Mar 2022) www.cog-genomics.org/plink/2.0/

Logging to /groups/users/output/common_snps/final_subset_pruned_data.log.

Options in effect:

--make-pgen psam-cols=fid,parents,sex,phenos

--out /groups/users/output/common_snps/final_subset_pruned_data

--pfile /groups/users/output/common_snps/subset_pruned_data

--rm-dup force-first

--threads 1

Start time: Fri May 13 07:47:10 2022

217778 MiB RAM detected; reserving 108889 MiB for main workspace.

Using 1 compute thread.

188 samples (85 females, 103 males; 188 founders) loaded from

/groups/users/output/common_snps/subset_pruned_data.psam.

56833 variants loaded from

/groups/users/output/common_snps/subset_pruned_data.pvar.

Error: PgfiInitPhase1() was called with raw_variant_ct == 56833, but

/groups/users/output/common_snps/subset_pruned_data.pgen

contains 56836 variants.

End time: Fri May 13 07:47:10 2022

Christopher Chang

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May 17, 2022, 11:52:33 AM5/17/22

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This means that your .pvar and .pgen files are out of sync with each other, which could happen if you e.g. removed a few lines from the .pvar without removing the corresponding variants from the .pgen.

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