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CMD_HELP.md

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Genome Nexus Annotation Pipeline

This tool has two subcommands: annotate, merge
To use it, you need to install Java version 8 or above.

The help page can be displayed simply by:

java -jar gnap.jar -h

The output will be

usage: GenomeNexusAnnotationPipeline annotate
annotate is the default behavior when a subcommand is omitted.
annotate subcommand options:
 -e,--error-report-location <arg>   Error report filename (including path)
 -f,--filename <arg>                Mutation filename
 -h,--help                          shows this help document and quits.
 -i,--isoform-override <arg>        Isoform Overrides (mskcc or uniprot)
 -o,--output-filename <arg>         Output filename (including path)
 -p,--post-interval-size <arg>      Number of records to make POST requests to Genome Nexus with at
                                    a time
 -r,--replace-symbol-entrez         Replace gene symbols and entrez id with what is provided by
                                    annotator
 -t,--output-format <arg>           extended, minimal or a file path which includes output format
                                    (FORMAT EXAMPLE:
                                    Chromosome,Hugo_Symbol,Entrez_Gene_Id,Center,NCBI_Build)
Visit https://github.com/genome-nexus/genome-nexus-annotation-pipeline/blob/master/CMD_HELP.md for
more.

usage: GenomeNexusAnnotationPipeline merge
merge subcommand options:
 -d,--input-mafs-directory <arg>   directory containing all MAFs to merge
 -h,--help                         shows this help document and quits.
 -i,--input-mafs-list <arg>        comma-delimited list of MAFs to merge
 -o,--output-maf <arg>             output filename for merged MAF [REQUIRED]
 -s,--skip-invalid-input           skips invalid input file. Input file must include following
                                   headers:Chromosome, Start_Position, End_Position,
                                   Reference_Allele. Input file should either include
                                   Tumor_Seq_Allele1 or Tumor_Seq_Allele2
Visit https://github.com/genome-nexus/genome-nexus-annotation-pipeline/blob/master/CMD_HELP.md for
more.

Let's go over all the subcommands and their options one by one!

Subcommand - annotate

This subcommand allows the annotation of genomic variants from a MAF file using Genome Nexus.
The help page for the subcommand annotate can be displayed simply by:

java -jar gnap.jar annotate -h

Let's go over the rest of the options of the subcommand annotate.

Options of the subcommand - annotate

  • -e, --error-report-location: filename which will be used for error reporting
java -jar gnap.jar annotate --filename in.txt --output-filename out.txt --error-report-location error.log

After the above command is completed successfully, a file named error.log, which includes info about failed annotations will be created.

  • -f, --filename: filename which will be annotated. File should be tab separated and valid.
java -jar gnap.jar annotate --filename in.txt --output-filename out.txt

After the above command is completed successfully, a file named out.txt, which includes all variants annotated successfully and unsuccessfully will be created.

java -jar gnap.jar annotate --filename in.txt --output-filename out.txt --isoform-override uniprot

After the above command is completed successfully, a file named out.txt, which includes all variants annotated successfully and unsuccessfully overridden by uniprot isoform, will be created.

  • -o, --output-filename: filename to which annotations will be written.
java -jar gnap.jar annotate --filename in.txt --output-filename out.txt

After the above command is completed successfully, a file named out.txt, which includes all variants annotated successfully and unsuccessfully will be created.

  • -p, --post-interval-size: number of maximum records in a single Genome Nexus POST request
    • Application uses a post interval size of 100 by default.
    • You can set this option to 1 to use Genome Nexus GET request
java -jar gnap.jar annotate --filename in.txt --output-filename out.txt --post-interval-size 500

The command above will send a list of 500 Genomic Locations per POST request.

  • -r, --replace-symbol-entrez: it enables the replacement of gene symbols and entrez id with what is provided by the annotator
java -jar gnap.jar annotate --filename in.txt --output-filename out.txt --replace-symbol-entrez
  • -t,--output-format: it enables formatting of the output file based on a pre-defined format or based on a custom format.
    • minimal
      • It will produce an output file with 3 header groups:
        1. the headers of input file
        2. any additional headers (sorted alphabetically)
        3. the header named Annotation_Status
    • extended
      • It will produce an output file with the headers of the extended MAF format (a-c) plus additional headers (d-e):
        1. 32 columns from the TCGA MAF format
        2. 1 column with the amino acid change
        3. 4 columns with information on reference and variant allele counts in tumor and normal samples
        4. any additional headers (sorted alphabetically)
        5. the header named Annotation_Status.
    • custom format file
      • A file containing a single line of headers separated with comma.
      • It will produce an output file with 2 header groups:
        1. the headers of format file
        2. the header named Annotation_Status
java -jar gnap.jar annotate --filename in.txt --output-filename out.txt --output-format format.txt

Let's assume the content of the format.txt file is: Chromosome,Hugo_Symbol,Entrez_Gene_Id,Center,NCBI_Build After the above command is completed successfully, a file name out.txt will be produced with the above 5 headers.

Subcommand - merge

This subcommand merges given MAF files or the files in a given directory, using their headers, into a single MAF file.

The help page for the subcommand merge can be displayed simply by::

java -jar gnap.jar merge -help

Let's go over the rest of the options of the subcommand merge.

Options of the subcommand - merge

  • -d, --input-mafs-directory: The directory name which homes MAF files to be merged. MAF files doesn't have to be valid.
java -jar gnap.jar merge --input-mafs-directory MAF_DIR --output-maf out.txt
  • -i, --input-mafs-list: comma-delimited list of MAF files to be merged. Prefer to use the option input-mafs-directory in case of many files.
java -jar gnap.jar merge --input-mafs-list file1,file2,file3 --output-maf out.txt
  • -o, --output-maf: The name of the output file
java -jar gnap.jar merge --input-mafs-list file1,file2 --output-maf out.txt

The command above will merge file1 and file2 based on their headers and will write to the file named out.txt

  • -s, --skip-invalid-input: It enables to skip invalid MAF files.
java -jar gnap.jar merge --input-mafs-directory MAF_DIR --output-maf out.txt --skip-invalid-input

The command above will select the valid files inside the folder named MAF_DIR first, and then it will merge all of them based on their headers. Finally, it will write to the file named out.txt

Appendix

Definition of Valid Input File

A valıd input file should include the following headers: Chromosome, Start_Position, End_Position, Reference_Allele and should include one of these headers: Tumor_Seq_Allele1, Tumor_Seq_Allele2
A valid input file with only the headers mentioned above is called minimal file.