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.
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} ${dir}/${tumorbam} \ -o ${tumor}${normal}.octopus.vcf.gz \ -N ${normal}