5. Make Single Source File (`makedata`)¶

After downloading data source files, basically you don’t have to make the single source file. But you want to manage the source files more efficiently, you can make a single source file from serveral source files.

mutanno makedata \
        -ds data_structure.json \
        -out single_datasource_file.tsi \
        -vartype SNV \
        -blocksize 1000

5.1. Input file¶

To make single source file, MutAnno requires a data structure file (-ds) and data source files that the structure file contains.

5.1.1. Data structure file¶

The data structure file must include data source file path.

5.1.2. Data source file¶

You can download various data source files. Please see here. Each source file path should be inserted in the structure file.

{
  "name": "MUTANNO",
  "source": [
    {
      "name": "DBSNP",
      "version": "20190722",
      "version_date": "07/22/2019",
      "sourcefile": "ANNOTATION_SOURCE/GRCh38_latest_dbSNP_all.convchrom.onlyid.vcf.gz",
      "format": "tsi"
    }
   ]
 }

5.2. Output file¶

With -out option, you can assign the output file name and path for the single source file.

5.3. Annotation type¶

By default, -vartype is SNV among SNV, GENE, and CODING_GENE_MAIN_CHROM.

5.3.1. SNV¶

5.3.2. GENE¶

To make gene anntoation file, we can use

5.3.3. CODING_GENE_MAIN_CHROM¶

5.4. Only for specific genomic region¶

If you want to make the single annotation file for specific genomic region, you can use -region option.

mutanno makedata \
        -ds data_structure.json \
        -out single_datasource_file.tsi \
        -vartype SNV \
        -blocksize 1000
        -region chr1:1000000-2000000

5. Make Single Source File (makedata)¶