I have used the UnifiedGenotyper to call variants on a set of ~2400 genes (TruSeq Illumina data) from 28 different samples mapped against a preliminary draft genome. I do not have a defined set of SNPs or INDELs to use in recalibration via VQSR.
While the raw VCF has plenty of QUAL scores that are very high, not a single call has a PASS associated with it in the Filter field- all are "." If I use SelectVaraints to filter the VCF based on high QUAL or DP values, or combination, the Filter field remains "." for the returned variants.
Am I doing something wrong, or is the raw file telling me that none of the variant calls are meaningful, in spite of their high QUAL values?
Is there a "best practices" way to go about filtering such a dataset when VQSR can't be employed? If so, I haven't found it.