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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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Question - RNASeq tumour-normal data and variant calling #3523

Closed VictoriaPatten closed 2 years ago

VictoriaPatten commented 3 years ago

Hi there, is there a specific pipeline for matched tumour-normal RNA-Seq data or should one follow the yaml file set up for the 'Somatic (cancer) variants' as per the documentation pages? I couldn't seem to find a specific set-up under 'bulk-RNA-seq'.

Also, which tool would be best to use for variant calling? I read that vardict results might be uncertain and mutect2 not supported?

Thanks in advance.

naumenko-sa commented 3 years ago

Hi @VictoriaPatten!

Unfortunately, we don't have T/N calling for RNA-seq. Even N calling is tricky in RNA-seq (precision could be quite low especially for indels, gatk3.x is recommended over gatk4). You may try to call T and N separately with gatk or vardict and then subtract the variants as the first approximation.

Sergey

VictoriaPatten commented 3 years ago

@naumenko-sa Thank you for the info and advice. Much appreciated.