How to detect somatic mutations with allele frequencies lower than 0.05?

Illumina / strelka

Strelka2 germline and somatic small variant caller

GNU General Public License v3.0

356 stars 104 forks source link

How to detect somatic mutations with allele frequencies lower than 0.05? #147

Open DavidAustinNix opened 5 years ago

DavidAustinNix commented 5 years ago

Hello Folks,

Strelka2 is our go to caller for standard somatic variant calling. It works well down to about 5% AF. We'd like it to work with our ctDNA variant calling where the read depth exceeds 3K and the allele frequencies are 1- 0.1% . When testing with simulated datasets, Strelka2 appears to stop emitting variants as the AF of the spikes approaches 1%.

Any suggestions for how to relax the stringency of the emitted calls? Some extraStrelkaArguments settings?

Thanks, David

DavidAustinNix commented 5 years ago

By executing Strelka/2.9.10/libexec/strelka2 a whole collection of options are available to be modified that seem to be relevant.

Yet when adding these to the Strelka/2.9.10/bin/configureStrelkaSomaticWorkflow.py.ini config file as "extraStrelkaArguments = --strelka-snv-min-qss-ref 0", no change in output is seen.

Any ideas?