How to detect germline mutations with fractions lower than 0.2?

[wangshun1121]

I use strelka2(v2.9) with default parameters (added --exome) to detect variants in panels, there are many variants with low allele frequencies(<0.2 or even lower). Almost all variants with freq>0.2 were detected, but variants with lower freq are missed.

Then are there any parameters available to make strelka2 more sensitive for low freq variants?

[wangshun1121]

I tried to use simulated reads or normal reads (e.g, reads of NA12878) as normal, panel sequences as "tumor", using strelka2 somatic method to call variants. I can get variants of frequencies less than 5% using this way.

I wonder if strelka2 Germline can add a parameter to filter allele fraction like freebayes ?