How to detect somatic mutations with allele frequencies nearly 0.01?

Illumina / strelka

Strelka2 germline and somatic small variant caller

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How to detect somatic mutations with allele frequencies nearly 0.01? #225

Open wuyuling327 opened 1 year ago

wuyuling327 commented 1 year ago

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 commented 1 year ago

--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