<commit_before>GENERAL INFORMATION

This tool is designed to oncotate MAF files by using the Oncotator web service
provided by the Broad Institute (http://www.broadinstitute.org/oncotator/).

This command line tool enhances a MAF file by adding 5 new columns for each line
by processing the result of a oncotator query.

USAGE

Oncotator needs a properties file (db.properties) for database settings. You can find
an example properties file (db.properties.EXAMPLE) under the resources directory of this module.
Put db.properties together with the bash script (oncotateMaf.sh) and the executable jar file
(oncotator.jar) into the same directory.

Run the bash script as:

	./oncotateMaf.sh <input_maf_file> <output_maf_file>

Note that the bash script requires the name of the jar file to be oncotator.jar.
So, rename the jar file if necessary. Alternatively, you can also run the executable jar
directly by using java -jar command:

	java -jar <jar_file> <input_maf_file> <output_maf_file>

It is also possible to run the oncotator tool without connecting to a database. In this case,
it will access to the Oncotator Web Service for each entry. The execution syntax without
a database connection is:

	./oncotateMaf.sh -nodb <input_maf_file> <output_maf_file>

INPUT FORMAT

In order to execute successfully, this tool needs the input MAF to satisfy the following conditions.

	- NCBI build of the MAF should be 37 (hg19) because Broad's oncotator service works only with hg19.
	If there are too many entries with incorrect build number, the program terminates without trying to
	oncotate all entries.
	- It must have these 6 standard column headers: Chromosome, Start_Position, End_Position,
	Reference_Allele, Tumor_Seq_Allele1, Tumor_Seq_Allele2, and NCBI_Build.
	- The data for each entry under these 6 data columns should conform to standard MAF specification.
	See https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+%28MAF%29+Specification
	for details.

OUTPUT FORMAT

The output produced by this tool will contain 5 additional columns named: ONCOTATOR_VARIANT_CLASSIFICATION,
ONCOTATOR_PROTEIN_CHANGE, ONCOTATOR_COSMIC_OVERLAPPING, ONCOTATOR_DBSNP_RS, and ONCOTATOR_GENE_SYMBOL.

If the input file already contains these oncotator columns, the tool will overwrite the data under these
columns.

STANDARD OUTPUT INFORMATION MESSAGES

This tool prints each key generated for each data row to the standard output. It also prints any error
message generated by Broad's oncotator service.

PROGRAM TERMINATION

The tool terminates with a non-zero code if there is no error during the process. It will also
print the number of errors to the standard output at the end of the process.<commit_msg>latest pull<commit_after>GENERAL INFORMATION

This tool is designed to oncotate MAF files by using the Oncotator web service
provided by the Broad Institute (http://www.broadinstitute.org/oncotator/).

This command line tool enhances a MAF file by adding 5 new columns for each line
by processing the result of a oncotator query.

USAGE

Oncotator needs a properties file (db.properties) for database settings. You can find
an example properties file (db.properties.EXAMPLE) under the resources directory of this module.
Put db.properties together with the bash script (oncotateMaf.sh) and the executable jar file
(oncotator.jar) into the same directory.

Run the bash script as:

	./oncotateMaf.sh <input_maf_file> <output_maf_file>

Note that the bash script requires the name of the jar file to be oncotator.jar.
So, rename the jar file if necessary. Alternatively, you can also run the executable jar
directly by using java -jar command:

	java -jar <jar_file> <input_maf_file> <output_maf_file>

It is also possible to run the oncotator tool without connecting to a database. In this case,
it will access to the Oncotator Web Service for each entry. The execution syntax without
a database connection is:

	./oncotateMaf.sh -nocache <input_maf_file> <output_maf_file>

INPUT FORMAT

In order to execute successfully, this tool needs the input MAF to satisfy the following conditions.

	- NCBI build of the MAF should be 37 (hg19) because Broad's oncotator service works only with hg19.
	If there are too many entries with incorrect build number, the program terminates without trying to
	oncotate all entries.
	- It must have these 7 standard column headers: Chromosome, Start_Position, End_Position,
	Reference_Allele, Tumor_Seq_Allele1, Tumor_Seq_Allele2, and NCBI_Build.
	- The data for each entry under these 7 data columns should conform to standard MAF specification.
	See https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+%28MAF%29+Specification
	for details.

OUTPUT FORMAT

The output produced by this tool will contain 5 additional columns named: ONCOTATOR_VARIANT_CLASSIFICATION,
ONCOTATOR_PROTEIN_CHANGE, ONCOTATOR_COSMIC_OVERLAPPING, ONCOTATOR_DBSNP_RS, and ONCOTATOR_GENE_SYMBOL.

If the input file already contains these oncotator columns, the tool will overwrite the data under these
columns.

STANDARD OUTPUT INFORMATION MESSAGES

This tool prints each key generated for each data row to the standard output. It also prints any error
message generated by Broad's oncotator service.

PROGRAM TERMINATION

The tool terminates with a non-zero code if there is no error during the process. It will also
print the number of errors to the standard output at the end of the process.
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