Merge pull request #3 from rmadupuri/main

Added docker source to readme

README.md

@@ -24,7 +24,7 @@ python 3
 
 ### Running the tool 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. 
@@ -35,6 +35,21 @@ 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
+
+Usage:
+```
+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
+```
+- `-v ${PWD}:/wd`: This option maps the current working directory on local machine to the /wd directory inside the Docker container. This allows files in the local directory to be accessed from within the container.
+- `--input-data /wd/test.vcf`: This option specifies the input file location at /wd/test.vcf.
+- `--output-directory /wd/maf/`: This option specifies the output directory where the maf files will be saved. The files will be created at /wd/maf.
+
 ### Resolving allele counts:
 
 vcf2maf_lite supports the following VCF pipelines/methods for resolving the allele counts: