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We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
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,