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README.md

Mouse Exome Sequencing Variant Calling

This repository documents a pipeline for somatic variant calling from mouse exome sequence data. It is for my own research use, but may act as a guideline for anyone looking to do accomplish the same goal. The pipeline is based on the Broad Institute's best practices.

Note: This pipeline was built in 2016, and has not been actively updated since. Some aspects of the pipeline may therefore be outdated.

This repository is organized as follows:

Install           Instructions on installing the necessary frameworks
ReferenceFiles    Instructions on downloading and processing the necessary reference files
VariantCalling    Pipeline for variant calling (including preprocessing and annotation)

The exome sequencing data I use for this project was generated using an Illumina HiSeq X10 with the Agilent SureSelect Mouse All Exon Kit. The tissue used was collected from FVB/NJ mice, which is reflected in the choice of SNP and InDel files. All analyses are performed on a Unix-based operating system.

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A pipeline for variant calling from exome sequence data from murine tumors.

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