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Generating a vcf with the information of specific genome positions (hotspots)
I'm developing a pipeline that needs to take into account the information about variants that are present on a list of hotspots on the genome, because my final analysis uses the information contained on the vcf.
I'm working with WES data, and although I can use as input a bed file with the regions to be analyzed, if the genome region on my hotspot list is showing the same base as the reference genome, it won't appear on my vcf.
So when I filter my vcf for the specific variants on my list, I don't know if the variants that are not present on the file aren't present because it is showing the same base as the reference genome, or because there was a low coverage for the sample on these regions.
I was wondering if GATK best practices pipeline could offer the option to input the list of hotspot so it could generate a vcf with the information for these variants.
If not, what could be the best approach to solve it, and still use GATK's pipeline.
I appreciate the attention,