added docker source

docs/Annotate-VCF-File.md

@@ -6,31 +6,9 @@ Before annotating a VCF file using Genome Nexus, it must be first converted to a
 
 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.
 
-### Requirements
-
-```
-python3
-click
-```
-Python `click` module can be installed using `pip install click`.
-### Usage
-
-```
-python3 vcf2maf_lite.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]
-  -a | --retain-info            Comma-delimited names of INFO fields to retain as extra columns in MAF [optional]
-  -f | --retain-fmt             Comma-delimited names of FORMAT fields to retain as extra columns in MAF [optional]
-```
-
 ### Minimal Example
 ```
-python3 vcf2maf.py --input-data /data/vcf --output-directory /data/maf/ --center-name 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
+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 /vcf folder to MAF format. 
@@ -41,6 +19,18 @@ This command converts the VCF files in /vcf folder to MAF format.
 - 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), 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.