sample query for the variants in a particular gene?

[burcd...@gmail.com]

Dear all,

I am wondering if there is any possibility to search for the samples carrying variants in a particular gene ?

I could not found in your user guide.

If you could help me, I would be grateful.

Thanks.

Best,

[Aaron Quinlan]

You can use the —show-samples option: https://gemini.readthedocs.io/en/latest/content/querying.html#show-samples-finding-out-which-samples-have-a-variant

For example:

$ gemini query --header --show-samples -q "select chrom, start, end, ref, alt \
                                from variants where gene = ‘TP53’ limit 5" test.query.db

[burcd...@gmail.com]

Hello Aaron,

thanks for your reply.

I tried to get detailed information corresponding to the variants in the particular genes, which I got after running the command you specified in your message, however, each time got an error.

Could you please tell me what is the exact command I should run. I tired for instance the code below and got an error.

gemini query --header --show-samples -q "select v.gene, g.transcript_status, g.transcript, \
               v.impact from variant_impacts v, gene_detailed g \

                               WHERE v.transcript = g.transcript AND \
                                           v.gene = g.gene AND \
                                             v.gene = 'TP53' \
                         v.impact_severity!='LOW'"    db

Thanks for your help.

[Aaron Quinlan]

Just to clarify you should remove the “limit 5” clause, as that will solely report the first 5 rows meeting your query criteria.

Aaron