Genomic Pipeline is a software used for analyzing DNA sequence data.

The chart below shows the workflow of the pipeline.

• UNIX/Linux
• Python 3 or higher
• Picard
• GenomeAnalysisToolkit (GATK 3.5-0)
• VarScan.v2.3.9
• Samtools

$git clone https://github.com/MBaysanLab/GenomicPipeline

If you do not have git you can download zipped Genomic Pipeline here.

$cd genomics_pipeline
$python gui.py

You can now

• Select mapping, variant calling or full pipeline,
• Enter your working directory and decide which algorithm you want to use for mapping and variant calling,
• Choose a library ID and germline folder. Then you can start processing your data via submit button. The final VCF file will be saved in your working directory.

If you have questions or need help using the pipeline you can contact us via e-mail