TCGA tumor/normal RNA-seq somatic mutation calling

Question

[umn_bist]

I am wondering if there is a publicly available pipeline that automates preprocessing QC, alignment, postprocessing QC, calling variant.

At the moment I have >100 tumor/normal PE RNA-seq samples from TCGA.

I am manually piping these samples through cutadapt --> prinseq --> STAR --> picard --> GATK, but was wondering if there is a single (wrapper) solution to handle large volumes of data.

Answer 1

[Roman Valls Guimerà]

Perhaps you can give a try to this one?

Answer 2

[igor]

There are a lot of available pipelines, but you will usually end up spending more time configuring them and resolving various dependencies than it would take you to build your own. Shared pipelines start to make sense when you are handing a lot of projects or work in a group.