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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
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Doubts with polyclone module #111

Closed evergmillan closed 4 years ago

evergmillan commented 4 years ago

Hello, I ran octopus with dengue viral genome against a genomic sample from three regions of interest.

I ran octopus as follows:

$ octopus -R DENV1RefSec.fasta -I DENV1-02_final_map_filtered_sorted_add_groups.bam -o DENV1_02_PE.vcf --bamout DENV1_02_flags_PE.bam -C polyclone

The program output shows the following line:

The polyclone calling model is still in development. Do not use for production work!

I have 2 questions:

Thank you

Version

$ octopus --version
octopus version 0.7.0 (develop 2c756ec)
Target: x86_64 Linux 4.15.0-62-generic
SIMD extension: AVX2
Compiler: GNU 9.2.0
Boost: 1_72
dancooke commented 4 years ago

The warning is there as this calling model has not been tested. There are also no pre-trained random forest models provided for viral or bacterial data - you can use the germline forest but there are no guarantees about performance. Basically we're making no claims about accuracy; you should validate yourself.

dancooke commented 4 years ago

Closing due to inactivity. Please re-open if needed.