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icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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including SNV/indel calling on RNA-seq data #61

Closed zktuong closed 1 year ago

zktuong commented 1 year ago

hi, was wondering if the RNA-seq SNV variant calling for RNA-seq data is performed during the pipeline? If not, can this be added into future version?

https://gatk.broadinstitute.org/hc/en-us/articles/360035531192-RNAseq-short-variant-discovery-SNPs-Indels-

riederd commented 1 year ago

Hi, thanks for the suggestion, however, the proposed GATK pipeline/workflow is not suitatable to call somatic mutations, it would also call any germline mutation which are not necessarily specific to the tumor, which in turn would produce antigen predictions which are not specific to the tumor.