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Finding variants within a subset of a BAM file

I downloaded bam "slices" from a database (TCGA), which correspond to a subset of the entire alignment, corresponding to a small set of genes. Now I would like to find variants in the human genome, I am currently using strelka and it works fine. However, I am wondering if there is a more efficient way to do it given that I know exactly the region of interest (those few genes)? Do you recommend me subsetting the human genome to only those genes? What tool should I use to do that?

variant calling
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written by ramiro.barrantes • ramiro.barrantes

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written by Pierre Lindenbaum Pierre Lindenbaum

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However, I am wondering if there is a more efficient way to do it given that I know exactly the region of interest (those few genes)?

https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md

Strelka calls the entire genome by default, however variant calling may be restricted to an arbitrary subset of the genome by providing a region file in BED format with the --callRegions configuration option.

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written by Pierre Lindenbaum Pierre Lindenbaum

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