Merge pull request genome-nexus#742 from rmadupuri/master

Update VCF2MAF annotation readme

docs/Annotate-VCF-File.md

@@ -4,40 +4,33 @@ Before annotating a VCF file using Genome Nexus, it must be first converted to a
 
 ## VCF to MAF conversion
 
-To convert a Variant Call Format (VCF) file to Mutation Annotation Format (MAF), we recommend using the [vcf2maf Python tool](https://github.com/genome-nexus/annotation-tools/blob/master/vcf2maf.py).
-
-This tool is designed to support the conversion of VCF files from multiple callers to a standardized MAF format that can be easily used for downstream analysis. Note that this Python script is a rewritten version of the [vcf2maf Perl tool](https://github.com/mskcc/vcf2maf).
-
-### Requirements
-
-```
-python3
-click
-```
-Python `click` module can be installed using `pip install click`.
-### Usage
-
-```
-python3 vcf2maf.py --help
-
-  -i | --input-data             A list of .vcf files or input data directories, separated by commas [required]
-  -o | --output-directory       output data directory [optional]
-  -c | --center                 name of the center (standard MAF field = 'Center') [optional]
-  -s | --sequence-source        Sequencing source (standard MAF field = 'Sequencing_Source'), e.g., WXS or WGS [optional]
-  -t | --tumor-id               The ID of the tumor sample utilized in the genotype columns of the VCF file. [optional]
-  -n | --normal-id              The ID of the normal sample utilized in the genotype columns of the VCF file. [optional]
-```
+To convert a Variant Call Format (VCF) file to Mutation Annotation Format (MAF), we recommend using the [vcf2maf-lite Python tool](https://github.com/genome-nexus/vcf2maf-lite). It is a lightweight Python adaptation of the [vcf2maf Perl tool](https://github.com/mskcc/vcf2maf), that converts the VCF to MAF format without adding variant annotations.
 
 ### Minimal Example
 ```
-python3 vcf2maf.py --input-data /data/vcfs --output-directory /data/maf/ --center-name CTR --sequence-source WGS --tumor-id Tumor --normal-id Normal
+python3 vcf2maf.py --input-data /data/vcf --output-directory /data/maf/ --center CTR --sequence-source WGS --tumor-id Tumor --normal-id Normal --retain-info Custom_filters,AC,AF,AC_nfe_seu,AC_afr,AF_afr --retain-fmt alt_count_raw,ref_count_raw,depth_raw
 ```
-This command converts the VCF files in /vcfs folder to MAF format.
+
+This command converts the VCF files in /vcf folder to MAF format. 
 - The `--input-data` option is used to specify either a single VCF file or a directory containing multiple VCF files (separated by commas). This option supports passing multiple input files or directories at once.
-- The `--output-directory` option allows you to specify the directory where the MAF files will be saved. If no output path is provided, the default output directory `vcf2maf_output` will be used in the current working directory.
+- The `--output-directory` option allows you to specify the directory where the MAF files will be saved. If no output path is provided, the default output directory `vcf2maf_output` will be used in the current working directory. 
 - The `--tumor-id` option allows you to specify the ID of the tumor sample used in the genotype columns of the VCF file. If the option is not used, the script will automatically identify the tumor ID from either the `tumor_sample` keyword in the meta data lines or the sample columns from VCF header.
 - The `--normal-id` option allows you to specify the ID of the normal sample used in the genotype columns of the VCF file. If the option is not used, the script will automatically identify the normal ID from either the `normal_sample` keyword in the meta data lines or the sample columns from VCF header.
+- The `--retain-info` option allows you to specify the INFO fields to be retained as additional columns in the MAF. If the option is not used, standard MAF columns are included by default.
+- The `--retain-fmt` option allows you to specify the FORMAT fields to be retained as additional columns in the MAF. If the option is not used, standard MAF columns are included by default.
+
+### Convert with Docker
+
+vcf2maf-lite is available in DockerHub at https://hub.docker.com/r/genomenexus/vcf2maf-lite
+
+```
+docker pull genomenexus/vcf2maf-lite:main
+docker run -v ${PWD}:/wd genomenexus/vcf2maf-lite:main python3 vcf2maf_lite.py --input-data /wd/test.vcf --output-directory /wd/maf/ --center CTR --sequence-source WGS --tumor-id Tumor --normal-id Normal --retain-info Custom_filters,AC,AF,AC_nfe_seu,AC_afr,AF_afr --retain-fmt alt_count_raw,ref_count_raw,depth_raw
+```
+Output can be found in the /maf directory.
+
+
 
 ## Annotate a MAF file:
 
-Once the VCF file has been converted to Mutation Annotation Format (MAF), you can proceed to annotate the MAF files using Genome Nexus. Refer to the [Annotate a MAF File](https://docs.genomenexus.org/annotate-maf-file) section for detailed instructions.
+Once the VCF file has been converted to Mutation Annotation Format (MAF), the MAF file can be annotated using Genome Nexus. Refer to the [Annotate a MAF File](https://docs.genomenexus.org/annotate-maf-file) section for detailed instructions.