VCFEVal cannot found sample in multi-sample VCF

[Kübra Narcı]

Hi, I am comparing a series of samples in a multi sample VCF with a single sample containing VCFs. I can compare every sample in the multi-sample VCF with its companient (same sample name), but not the last sample (in the header). I am sure the sample is inside the VCF file and I am sure that I am comparing true single VCF (same sample name). 

Moreover, I reproduce this error with trying different ordered samples and issue is the same VCEval cannot found the last sample of multi-sample VCF. 

 Error: Sample "NA18874" not found in calls VCF.

Best,

Kübra Narcı

[Sean Irvine]

Hi Kübra,

I cannot be sure of your problem without more information, but it sounds like your calls VCF file is not correctly formatted.  How are you making that file?

You can try,

rtg vcfstats --sample NA18874 calls.vcf.gz

to check whether the specified sample is in the VCF file.

Also, you can try,

zgrep -m1 '^#CHROM' calls.vcf.gz

and check that the sample name appears in the list.

Otherwise, please post the exact command lines you are running, and if possible the header lines from the calls and baseline VCF files.

Hope this helps,

Sean.

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[Kübra Narcı]

I have also regenerated the error using two methods; 

1. I got a subset of samples from a big VCF file  (bcftools view with a sample list)

2. using bcftools merge to merge a series of VCFs

rtg vcfstats runs correctly with the sample.

Note: I performed by comparison successfully by simply subsampling the problematic sample and re-running vcfeval with it. 

Thanks 

Kübra Narcı

PhD Candidate

Department of Health Informatics 
Middle East Technical University 

[Len Trigg]

Hi Kübra,

Can you please attach a small baseline VCF and call VCF so we can replicate your error message here? (The VCF files probably only need to contain a single variant). Please also paste the exact command line that shows the problem with your example VCF files.

Cheers,

Len.

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