How to detect somatic mutations with allele frequencies nearly 0.01?

[wuyuling327]

I want to detect the ctdna indel which frequency is ~1%(4000X), and I have tried the param --candidate-indel-input-vcf which have inclued the indel, but the strelka indel result still not reserve the indel.
I used the strelk2 latest version v2.9.10. And I alse tried to modify the Strelka/2.9.10/libexec/strelka2 all options, but is not useful.
Any suggestions to increase the strelka2 indel sensitivity?

[lmanchon]

--Hi,

same problem, i can't detect SNV with VAF < 3%.
How to adjust that in the .ini config file ?
``
configureStrelkaGermlineWorkflow.py.ini file:

[StrelkaGermline]

maxIndelSize = 49

minMapq = 20

isWriteRealignedBam = 0

extraVariantCallerArguments =

extraStrelkaArguments = -used-allele-count-min-qscore 20 -min-qscore 10 --strelka-snv-min-qss-ref 0

``