Whole Exome sequenincg Variant Priortization

Question

[manojkumarbioinfo]

I'm new to NGS data analysis, can anyone suggest me free tools for prioritizing my Variants from the Whole-exome sequencing VCF file.

I have annotated my WES VCF file using annovar for prioritizing I'm using different cutoff such as frequency less than 1%, CADD score greater than 15 GERP score greater than 5 Polyphen, SIFT, Mutpred as deleterious

Answer 1

[chakk]

It really depends on what you are looking for. If you are looking for rare and disease causing variant then applying the filters you have described is a good start. Unfortunately there is no perfect way to filter data but I would suggest to think about the biology you are trying to explain (eg if a rare disease then make sure you frequency reflects that I would lower the AF filter).