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Calling variants on whole exome and whole genome samples together?
I have 15 affected samples. 2 are whole exome and 13 are whole genome. They have already been realigned on a single-sample level and had BQSR performed. I am contemplating running UnifiedGenotyper on all 15 samples together because we would like to compare the calls across the samples (especially in the coding regions). I am aware that there would be a large number of variant calls in the whole genome samples that would have little to no coverage in the exome samples. I haven't been able to find any posts that say you should or shouldn't run whole genome and exome samples through UnifiedGenotyper together. Are there any reasons why this should be discouraged?
Also, assuming I do perform multi-sample calling across all 15 samples, would it be ok to run that multi-sample VCF file through VQSR?