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VQSR on specific genomic region
Dear GATK Team,
I have exome-data of many individuals (>2000) called with the HaplotypeCaller, but only of a specific set of genes from the genome. I would like to apply the VQSR-tool to recalibrate my variants, but (as expected) I get back an error 'No data found'.
I know there is an option to 'pad' your data with other exomes, but then the generation method needs to be comparable to my dataset (which whole-exome-sequencing is not).
Alternatively, I was therefore wondering if there is an option to 'focus' the VQSR-tool only on specific regions of the genome/exome?
Because I know for sure that if only my regions would be considered in the recalibration I would have enough variants to create a recalibration model.
Thank you for your help in advance,