Entering edit mode
3.1 years ago
pt.taklifi
▴
60
Hello everyone I have some mutect2 vcf files . Unfortunately the quality column is not reported ( the value of QUAL for all variants is NA) and some variants have very low depth ( for example 1 ALT , 0 REF ) I was wondering if I could add quality to vcf files myself? if not, to remove low depth variants myself , what threshold of depth should I consider as a cut off
Hello,
The quality score should be calculated by the variant caller and it would not be a good ideia to input it yourself since you may don't have all the information used by the variant caller to call each variant. The depth threshold will depend in your analysis. In clinical settings, the threshold for a somatic analysis would be usually greater than 200x. However if it is for academic purposes you could use less, however it would have an impact in variants with very low allele frequency.