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VQSR on exome of small specific population
I've asked this question at the workshop in Brussels, and I would like to post it here:
I'm working on an exome analysis on trio. I would like to run VQSR of filteration on the data. since this is an exome project, there are not a lot of varients, and therefore, as I understand. the VQSR is not accurate. You suggest to add more data from 1000Genomes or other published data.
The families that I'm working on belongs to a very small and specific population, and I'm afraid that adding published data will add a lot of noise.
What do you think, should I add more published data? change parameters such as maxGaussians? do hard filteration?