I have a VCF file with a lot of "Infinity" values for the QUAL parameter in several invariant sites. Other invariant sites does not have these values, but rather numerical values.
I need to get a numeric value of QUAL, including for invariant sites, but cannot operate with these Inf values, specially because I have noticed (using IGV) that these appear both in regions that seem to have good and bad coverage, so I'm to really able to distinguish if these are associated with high or low quality regions (it's probably unrelated to this).
It probably worth mention that that VCF file has been generated first by using GATK HaplotypeCaller for different samples, and then using GATK CombineGVCFs and GenotypeGVCFs for generating a unique multisample VCF file.
