How to restrict VCF variants using a gene list with the set function in SnpSift?

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Hello,

I am trying to restrict VCF variants using a gene list (text file) with the set function in SnpSift.
After annotating with ANOVAR and running through SnpEff for effect prediction we have been able to set the resulting vcf file against a text file “gene of interest list” using SnpSift. We used the command:

sample.vcf | java -Xmx4G -jar SnpSift.jar filter --set gene_of_interest_list.txt “ANN[0].GENE in SET[0]” > sample_set.vcf

I would like to be able to do this in Galaxy. In the tool for “SnpSift filter” there is no option to upload a text file to set a gene list against the vcf file.

How can I set a vcf file against a specific gene list in Galaxy?

Thanks for your help.

1 Like
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Hi @Tracey and thanks for a very good first question here,
you are right that the Galaxy wrapper doesn’t offer an option to specify a set file. Looks simply like oversight during tool wrapping for Galaxy to me.
I’ve opened https://github.com/galaxyproject/tools-iuc/issues/3349 to track progress on this, and I might be able to add this functionality over the week if nobody else takes this over first.

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Thank you so much!