--vcf-idspace-to _ and Error: Multiple instances of '_' in sample ID.

[ryanlayer]

I am not sure how to get around this issue.

time ./plink --make-bed --vcf foo.vcf.gz --out foo.vcf.gz.plink --allow-extra-chr --vcf-idspace-to _
PLINK v1.90b3d 64-bit (10 Feb 2015)        https://www.cog-genomics.org/plink2
(C) 2005-2015 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to foo.vcf.gz.plink.log.
129004 MB RAM detected; reserving 64502 MB for main workspace.
Error: Multiple instances of '_' in sample ID.

[chrchang]

"--const-fid 0" is probably the simplest way; it causes all family IDs to be set to "0", and individual IDs to be set to the ID in the VCF file. (The default behavior is to treat '_' as a delimiter between the FID and IID; this obviously has a problem with multiple underscores.)

I will modify the error message to suggest --const-fid as a workaround.