MAGI, cBioPortal, GATK, Genepattern, MuTect, Oncotater, MutSigCV

Question

[Shicheng Guo]

Trying to make a pipeline to make them together, any existed tools? It will be great if the pipeline can be ran in local server or GenepatternNotebook.

Bioinformatic am is to do the exome-wide sequencing or genome-wide sequencing based cancer mutation identification, annotation and analysis.

Thanks

[WouterDeCoster]

can be run in local

What does that mean?

Answer 1

[WouterDeCoster]

Many workflow system exist allowing you to chain multiple programs, of which the most popular are (AFAIK) Snakemake and Nextflow.