I have two VCF files. One was generated using Samtools mpileup and the other Freebayes. I would like to do an intersection of these two VCF files and combine them using VCFtools. I want to filter SNPs based on their quality score, but do not know of a good way to choose the quality score value to filter on for my data.
What is a general guideline for choosing the quality score threshold? Also, what other metrics should I take a look at? I'm working with metagenomics sequence data.