Reducing Indel False Positives in Somatic Variant Detection

[jasmin774]

Hello,

I am using Octopus to detect somatic variants, but I am encountering a high number of false positives, particularly with indels. In many cases, ALT alleles are also found in the Normal sample, contributing to these false positives.

I have two questions:

Are there any Octopus options or parameter adjustments that could help reduce indel false positives?
Is there a recommended approach for re-filtering the VCF based on allele frequency (or read depth) to further reduce false positives?
Any guidance would be greatly appreciated.

Thank you!

Octopus: version=0.7.4
Genome: mouse mm10

octopus
-R ${ref} --threads ${threads}
-I ${dir}/${normal_bam} ${dir}/${tumor_bam}
-o ${tumor}_${normal}.octopus.vcf.gz
-N ${normal}