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Filtering variants after calling on intervals - VQSR vs Hard-filter vs CNN
Hi. I have ~80-100 low-coverage (5-10X) WGS samples which I want to run through a joint genotyping (GVCF) workflow. I have "Halotype-called" (ERC GVCF) variants on my genes of interest using an interval list (contains 90 genes).
Will VQSR work with the final interval-subsetted VCF ? If no, would it help if I extended my intervals to cover a 100 more genes and extend the intervals further ? I'm very reluctant to call variants on the whole genome samples since I'm in a hurry and HaplotypeCaller takes too long (~6 hours).
PS I have one high coverage sample which I can download but would prefer not to.
Apart from that I have previously made calls on the same samples (but over the whole genome) by which I plan to use in my training set.