ANNOTATION SUITE FOR GENIE

Usage:

bash import-scripts/annotation_suite/annotation_suite_wrapper.sh

    -i | --input-directory               input data directory for processing mutation data files
    -o | --output-directory              output directory to write processed and annotated mutation data files to 
    -e | --error-directory               error directory to write failed annotation error reports to
    -m | --merged-mutation-file          path to write the merged mutation file for the center
    -c | --center-name                   name of the center being processed
    -s | --sequence-source               name of the sequence source used by the center (i.e., WXS, WGS)
    -p | --annotation-scripts-home       path to the annotation suite scripts directory

Arguments

Input Directory ( -i | --input-directory ) : This is the input directory where the unprocessed MAFs and/or VCFs can be found.

Output Directory ( -o | --output-directory ) : This is the output directory where the processed (standardized) and annotated MAFs will be written. Sub-directories within the output directory will hold the standardized MAFs and annotated MAFs. These sub-directories will be created if they do not already exist. Any existing files within the output-directory and subdirectories will be deleted when this script is run.

The standardized MAFs generated by standardize_mutation_data.py will be written to ${OUTPUT_DATA_DIRECTORY}/processed. The annotated MAFs from running the Genome Nexus annotation pipeline will be written to ${OUTPUT_DATA_DIRECTORY}/annotated.

Error Directory ( -e | --error-directory ) : This is the error directory where the failed annotation MAF error reports will be written. This is a sub-directory within the output directory which will hold the failed annotation error reports. This directory will be created if it does not already exist. Any existing files within the error-directory will be deleted when this script is run.

The failed annotation MAF error report generated from running the Genome Nexus annotation pipeline for each center will be written to ${OUTPUT_DATA_DIRECTORY}/errors/{CENTER}_error_reports.

Note that the error directory will still output an empty file with the expected error report headers even if there are NO FAILED ANNOTATIONS for a center.

Merged Mutation File ( -m | --merged-mutation-file ) : This is the filepath of the final (standardized and annotated) MAF. The annotation suite wrapper will call merge_mafs.py with the argument --input-mafs-directory that points to an input directory containing the annotated MAF(s) - within the scope of the annotation suite, this input directory will be ${OUTPUT_DATA_DIRECTORY}/annotated.

Center Name ( -c | --center-name ) : This is the center name to be used when standardizing the unprocessed MAF(s) and VCF(s). All records in all output MAFs will have the entered value set in the "Center" column.

Sequence Source ( -s | --sequence-source ) : The sequence source is a required field for a standard MAF as defined by the TCGA project. Accepted values are either WGS and WXS. For GENIE, WXS is used since GENIE samples are sequenced with targeted gene panels.

Annotation Suite Scripts Directory ( -p | --annotation-scripts-home ) : needs to point to the directory where the packaged Genome Nexus Annotation Pipeline JAR and annotation suite python scripts are located:

• merge_mafs.py
• standardize_mutation_data.py
• annotator.jar

Merging standardized and annotated MAFs from multiple centers

This suite of tools was designed with the AACR Project GENIE in mind, which receives mutation data from multiple centers. This annotation suite wrapper tool was designed such that it will need to be run individually for each center to generate a per-center MAF that has been standardized and annotated with Genome Nexus. These per-center MAFs can be merged to generate a single GENIE project MAF with one of the existing tools provided: merge_mafs.py

The MAF merging script supports two different input arguments for merging MAFs: (1) a comma-delimited list of MAF filenames and (2) an input directory containing all MAFs to be merged. Option (2) is used by the annotation_suite_wrapper.sh to generate a per-center MAF. Option (1) was added to facilitate the merge of the individual per-center MAFs to generate the final single MAF for GENIE that will be imported into the cBioPortal.

Germline files

If "germline" is in the filename then standardize_mutation_data.py will assume that the file contains germline data. This will set the value in the output MAF Mutation_Status column to "GERMLINE". Please follow this naming convention if the mutation data file(s) are germline data.

Contributing

See CONTRIBUTING for how to make contributions to this repo.