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Joint/batch variant calling when too few variants per sample
We are sequencing a set of regions that covers about 1.5 megabases in total. We're running into problems with VQSR -- VariantRecalibrator says there are too few variants to do recalibration. To give a sense of numbers, in one sample we have about 3000 SNVs and 600 indels.
We seem to have too few indels to do VQSR on them and have a couple of questions:
Can we combine multiple samples to increase the number of variants, or does VariantRecalibrator need to work on each sample individually?
If we do not use VQSR for indels, should we also avoid VQSR for the SNPs?
The other question is whether joint or batch variant calling across several samples would help us in this case?
Thanks in advance!