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Do you recommend the use of the -newQual parameter
I have read here the following
The current model for calculating QUAL has some flaws that manifest, among other things, as a tendency to excessively penalize singletons and doubletons (variants observed only in one or two samples in a cohort), especially at large cohort sizes. It also uses different and needlessly complicated logic for dealing with haploid, diploid and polyploid cases, leading to "amusing" inconsistencies. No one likes that.
Assuming it continues to behave well in our hands and yours (those of you who switch it on), it will be the default model in GATK 4. And then it will get documented in loving detail too, of course.
So, I have a couple of questions.
Do you still recommend using this parameter? It has not replaced the default in gatk4, correct?
Does it only take affect when analysing the samples together with HaplotypeCaller in "-ERC GVCF" mode and then feeding the samples into GenotypeGVCFs?
Do I need to switch it on in both tools HaplotypeCaller and GenotypeGVCFs? If so, also in any others (e.g, filtration steps)?
How does it take affect for Mutect2? There is also a similar parameter one can switch on, correct?