I am using gemini to query databases made from vcf files, which contain data from multiple samples. However, I need to query data only from one sample, (for which I currently use grep to filter the results and > it into a txt file).
I tried experimenting with the --sample-filter option in gemini, the documentation I found however says only:

gemini query --sample-filter "phenotype=2" -q "YOUR_QUERY"

db_info says the table samples contains name, but when I try doing

gemini query --sample-filter "name='S2'" -q "YOUR_QUERY"

I'll get error, that I have an syntax error in my query. I tried putting there "sample_name=='S2'" even tried other criteria, like sample_id, but couldn't get this work.

So please, do you know how should I get this work, or have any other advice?

Thank you very much.


1 Answer 1


I've found a possible workaround to my problem, I filter the vcf input file before loading it into the db by vcfkeepsamples from vcflib.

But I still don't know if the --sample-filter in gemini works, so if you have any ideas, it would be helpful.


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