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different QUAL for invariant and variant sites
Is there any way to make an equivalent filter on variant and invariant sites based on QUAL?. I want to apply a higher QUAL filter for variant sites since they have different distributions. I was thinking of a QUAL of 30-40 for invariant sites, but I needed to decide on a similar QUAL for variant sites. I was thinking one possibility was to get the correlation of QUAL values for close variant and invariant sites (within 2bp). However, although significant, this correlation is not very high, around 0.5.
If I use a very low QUAL for variant sites I will get too many false positive alt variants, especially singletons.