Is there a non-arbitrary criterion to filter variants based on their QUAL score?
I have developed many NGS pipelines to analised which one reports better results and I also need to develop a filtering strategy for a cardiac panel. The quality score distribution of my 171 variants is quite heterogeneous but in general, most of them showed high QUAL values. However, there are a few of them with very low and low scores. I need some reasons to support why for example I discard variants whose QUAL score un under 500. Is that possible based on only the distribution of these values in the total number of variants? Looking ALLISA protocol for panel analysis, I have seen very often the value 500 but I cannot find if this is just a random example or if this is based on some analysis.
This is for an assessment in which I was given 2 paired-end FASTQ files.
