--sample-diff problem specifying ids

[Michael]

Hello, 

   I am having trouble calling --sample-diff using the 'ids=sampleId1 sampleId2' 

For example executing:

./plink2 --vcf TBP_Walker_merged.vcf.gz --out TBP_Walker_merged.diff --allow-extra-chr --sample-diff 'id-delim=,' 'ids=SRR1158874,SRR1158890'

gives the output below with error: Error: --sample-diff 'base='/'ids=' require 2 or more space-separated sample

executing this same command using the file='samples.txt' with the same two samples works fine.   Any idea what is wrong?   I am working on a Mac.

 Thanks !

Output:

PLINK v2.00a3 64-bit (25 May 2021)             www.cog-genomics.org/plink/2.0/

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

Logging to TBP_Walker_merged.diff.log.

Options in effect:

  --allow-extra-chr

  --out TBP_Walker_merged.diff

  --sample-diff id-delim=, ids=SRR1158874,SRR1158890

  --vcf TBP_Walker_merged.vcf.gz

Start time: Mon Jun  7 15:52:19 2021

Error: --sample-diff 'base='/'ids=' require 2 or more space-separated sample

IDs.

[Ashish Jayamohan]

Hello,

I believe the id's need to be space separated, not comma separated.

Best,

Ashish J

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Regards,

Ashish Jayamohan

[Michael]

Thanks Ashish.   I did specify the --sample-diff 'id-delim=,'   in the command.  I also tried using spaces but that didn't seem to help.  

       Regards, 

          Michael 

[Christopher Chang]

id-delim= specifies the delimiter between PARTS of a sample ID (FID vs. IID vs. SID).

[Michael]

Unfortunately, I  still having problems with the --sample-diff command:   For example:

 ./plink2 --vcf all_TB2225_06022020_nc000962.merge.norm.snps.anno.vcf --out all_TB2225.diff --allow-extra-chr --sample-diff  'ids=SRR5152915 SRR5152916 SRR5152917 SRR5152918 SRR5152919 SRR5152920'

still results in error message:

Error: --sample-diff 'base='/'ids=' require 2 or more space-separated sample

IDs.

The ids listed are listed in the header of the VCF file.   Any advice is much appreciated.   Thanks, 

 Michael

[Christopher Chang]

Why are you quoting the "ids=" section?  That's confusing the argument parser.

[Michael]

That was the problem.   Thanks very much!

Michael