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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
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Cohort of low coverage unmatched somatic exome data #174

Closed njbernstein closed 3 years ago

njbernstein commented 3 years ago

Hi there,

For a cohort of unmatched somatic data should all samples be included in the same invocation of like so: octopus -R hs37d5.fa -I tumourA.bam tumourB.bam -C cancer where tumourA.bam and tumourB.bam are from separate individuals but with the same tissue. Does this allow octopus to identify common sequencing artifacts which you might find via a panel of normals?

or does the cancer functionality of octopus only operate on a single patient's samples at the same time?

dancooke commented 3 years ago

As stated in the docs, the cancer model assumes samples are from the same individual. Octopus does not support panel of normals.

njbernstein commented 3 years ago

Sounds good. Thanks!