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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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Added tool #3681

Open Talo07 opened 2 years ago

Talo07 commented 2 years ago

Hi all,

I am new to bcbio-nextgen. I can't find strelka. Would it be possible to add tools that do not exist. If yes, could you explain to me how I could add it?

Thanks in advance Talo

naumenko-sa commented 2 years ago

Hi @Talo07 ! We do have strelka in bcbio: https://github.com/bcbio/bcbio-nextgen/blob/master/bcbio/variation/strelka2.py https://github.com/chapmanb/cloudbiolinux/blob/master/contrib/flavor/ngs_pipeline_minimal/packages-conda.yaml#L360 https://bcbio-nextgen.readthedocs.io/en/latest/contents/somatic_variants.html SN

Titos789 commented 2 years ago

Thanks @naumenko-sa It is possible to use joint-caller with strelka in bcbio ? (I have a trio of WGS)

naumenko-sa commented 2 years ago

There is strelka wrapper in germline mode. It supports multiple bams: https://github.com/bcbio/bcbio-nextgen/blob/master/bcbio/variation/strelka2.py#L32 https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md#germline-configuration-example

You may try running them as a trio family call by specifying the same batch for all samples: https://bcbio-nextgen.readthedocs.io/en/latest/contents/germline_variants.html#workflow4-whole-genome-trio-50x-hg38

I have never validated strelka in germline mode myself. Usually, strelka is used for somatic calling, in combination with other callers (vardict, mutect2) to achieve greater sensitivity, so please let us know, how it goes!

SN