Issue with merging .ped & .fam files

[Mahan]

I'm trying to merge multiple .ped and .fam files for ch 1 to 22. My command is as follows:

PLINK v1.90b6.22 64-bit (16 Apr 2021)

Options in effect:

  --biallelic-only strict

  --merge-list Chr_list.txt

  --out Biobank1445_Merged

Chr_list has .ped & .fam file names in each row. 

Warning: Multiple chromosomes seen for variant '.'.

Warning: Multiple chromosomes seen for variant '.'.

Warning: Multiple chromosomes seen for variant '.'.

Warning: Multiple chromosomes seen for variant '.'.

Warning: Multiple chromosomes seen for variant '.'.

Performing single-pass merge (1445 people, 26732129 variants).

Error: Variant '.' is not biallelic. To obtain a full list of merge failures,

convert your data to binary format and retry the merge.

Please let me know how i can address this issue! 

Thanks in advance

[Christopher Chang]

plink 1.x --merge-list merges variants by ID.  If you don't assign your variants unique IDs, this is what happens.

--set-missing-var-ids provides one way to address this.

[Mahan]

Thanks for your suggestion Chris.  Let me try this!