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Added docker source to readme #3

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May 24, 2024
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Added docker source to readme #3

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0b28a80
added docker source to documentation
rmadupuri May 24, 2024
cb4261f
Merge remote-tracking branch 'refs/remotes/origin/main'
rmadupuri May 24, 2024
fb16dd6
Update README.md
rmadupuri May 24, 2024
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17 changes: 16 additions & 1 deletion README.md
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Expand Up @@ -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.
Expand All @@ -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:
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