Input CSV

Entrypoint: 'parser'

The fields required for the input CSV files are listed below. See example here.

Field name	Required	Description
software	yes	The software used to call this variant. Must come from VEP, STAR-Fusion, rMATS, CIRCexplorer, and REDItools.
alt_splic_type	no	Alternative splicing type. Required for rMATS. Must come from SE, A5SS, A3SS, MXE, and RI.
source	yes	Source of the variant. For example, gSNP, sSNV, Fusion, circRNA, etc
path	yes	Path to the variant file.

Entrypoint: 'gvf' or 'fasta'

Directly input of GVF files is also supported, which will skip all moPepGen parsers. In this case, the input CSV should contain only one column being the path to the GVF files. See here for example.

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