abedkurdi/wes_somatic repository overview

Whole-Exome Sequencing pipeline for the detection of somatic mutations, based on the best practices provided by Broad Institute. This Docker image requires a directory that contains a folder named "fastq", in which it should contain the paired-end FASTQ files. Each sample should have tumor and normal and the FASTQ files should have the following prefixes <sample_name>_tumor_R1.fastq.gz, <sample_name>_tumor_R2.fastq.gz, <sample_name>_normal_R1.fastq.gz and <sample_name>_normal_R2.fastq.gz.

You can also run the pipeline using only tumor data, using the same file prefixes: <sample_name>_tumor_R1.fastq.gz, <sample_name>_tumor_R2.fastq.gz

To run the pipeline, execute the following command: docker run -it -v /path/to/the/project_directory/:/data/ abedkurdi/wes_somatic:May8_2024