Comments (2)
Hey there,
We chose that threshold in part because a collaborator working on a similar consensus variant calling method found that it was an optimal balance of sensitivity and specificity. We accepted the tradeoff so that we could reduce false positives, especially in FFPE data. We found Strelka2 is a pretty lenient variant caller with default settings and we got a lot of noise with the default filtering in place.
Do you have examples of particular indels that are recurrently missing in the outputs, or is there no pattern to which indels drop out? Are they called robustly by SAGE?
Cheers,
Laura
from lcr-modules.
Hi Laura,
Thank you for those insights- that's really helpful.
Our initial output returned no indels when we used the somaticEVS threshold of 10. When we remove the threshold filtering, we get indels in the output, some of which are also called by SAGE. We're currently troubleshooting to find the optimal threshold for our data.
Thanks again for your thoughts and for the great suite of modules.
Kind regards,
Natasha
from lcr-modules.
Related Issues (20)
- Liftover issue regarding seq_type HOT 1
- SAGE doesn't handle `chr` prefixes correctly HOT 9
- StringTie HOT 1
- Oncopipe mis-handling unmatched normal IDs HOT 1
- Add unmatched samples to demo data HOT 1
- Update documentation HOT 1
- Documenting what each tool accomplishes
- Default unmatched normal bug HOT 2
- Harmonize all CNV caller modules and automatically convert seg files to projections HOT 2
- in_module is missing from some output rules
- Refactor the LymphGen module to run per-sample HOT 1
- Missing lymphgen script HOT 5
- Mutect2 edge case error HOT 2
- finalizing seg files have an issue with special genome builds HOT 3
- Ecotyper module needs wget conda environment HOT 2
- QC module does not report the per-chromosome coverage HOT 1
- Lofreq- no INDEL calling HOT 2
- ancient flag on all samples tsv prevents rerun of gistic2 HOT 1
- Demo doesn't dry-run as documented HOT 15
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