Hello all,

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?

Thanks!!!!