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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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Providing additional options (--rna) to strelka2 #3319

Open ashwathkumar-arcus opened 4 years ago

ashwathkumar-arcus commented 4 years ago

Hello,

Is it possible to provide addition command line options to the strelka2 part of bcbio. I am aware that mutect2 is able to take in additional options using the "resources:" information in yaml file. I have tried the below and this doesnt seem to be passing the options to strelka2.

resources: strelka2: options: ["options"]

Any help is appreciated. Thanks !

roryk commented 4 years ago

Hi @ashwathkumar-arcus,

We don't have that option for strelka2 but we could add it, which options are you wanting to add?

ashwathkumar-arcus commented 4 years ago

Hi @roryk,

I was exploring the possibility of running rna-seq variant calling pipelines using bcbio. I was interested in seeing if the option "--rna" can be used to run the pipeline for pre aligned and processed RNA-seq bam files.

Thanks !

roryk commented 4 years ago

Hi @ashwathkumar-arcus,

Sorry, we don't have support for that currently. We have RNA-seq variant calling pipelines implemented as part of the RNA-seq pipeline in bcbio, but it's not set up to do tumor-normal calls. We will be working on that later this year as part of our CZI grant though, and will look into Strelka.