I'm checking quality for SNPs and INDELs from vcf file. i'm using vcfutils.pl for filtering.
I'm considering two criteria right now, DP(read depth) and QUAL (SNP quality). Any other things i need to check for quality control ?
please provide me some reference to set standard threshold values for DP and QUAL for filtering.
what should be the maximum read depth ?
Is it required to do Variant Recalibration ?