SNP calling pipeline

Status: Alpha

Authors: Freerk van Dijk, Morris Swertz

Based on ​Broad GATK pipeline.

To perform the analysis as fast and good as possible the pipeline has been divided into several small processes. These processes are all numbered and can be found below, including commands, input and output files starting with pre-alignment and ending with variation calling & filtering.

• SnpCallingPipeline/ReferencePreparation
• SnpCallingPipeline/AlignmentAndCleaning
• SnpCallingPipeline/VariantCalling

Simplified Overview

This simplified overview this schema hides intermediate sort and indexing steps and only shows data inputs/outputs first time they occur.

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