Criteria for variant call

Question

[maricom]

Hi,

I'm doing variant calls of human genomic data for clinical research purposes (trying to find mutations that could cause cancers), and I'd like to know which criteria I should use to call the variants or not.

The human genomic data was acquired from whole blood samples, the sequence data was acquired using MiSeq, and variant calling was conducted using TruSeq Amplicon App in the BaseSpace.

There are a lot of factors to decide, for example, how many mutant read depths there are, how much mutant frequency there are...etc.

Could you give me some advice on this?

Thank you,

[Jeremy]

You can look for QD >= 2, where QD = QUAL/DP.

[maricom]

Thank you for your reply! I'll try to use the criteria!