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 Some aspects of the pipeline may therefore be outdated.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.