Recently published apps
We published two additional GDC workflows on the CGC - mRNA Analysis pipeline and Tumor-only Variant Calling pipeline.
The mRNA pipeline performs quantification analysis on raw RNA-Seq data (FASTQs or unmapped BAM files) with STAR for alignment and HTseq for counting.
The Tumor-only Variant Calling workflow utilizes GATK4's MuTect2 to call variants on tumor samples. The workflow is used for for harmonization of genomic data for datasets such as The Cancer Genome Atlas (TCGA).