Allele-specific alignment sorting

See the documentation: https://felixkrueger.github.io/SNPsplit

Update December 2022:

SNPsplit has now been updated to work with new release of the Mouse Genomes Project. This means that it will now assume the GRCm39 mouse genome build by default, and use the latest SNP annotation file (v8: mgp_REL2021_snps.vcf.gz).

Installation

SNPsplit is written in Perl and is executed from the command line. To install SNPsplit simply download the latest release of the code from the Releases page and extract the files into a SNPsplit installation folder.

SNPsplit requires the following tools installed and ideally available in the PATH:

• Samtools

Documentation

The SNPsplit documentation can be found here: SNPsplit User Guide

Links

• SNPsplit publication at F1000 Research:
  • https://f1000research.com/articles/5-1479/v2
• Here is a link to the SNPsplit project site at the Babraham Institute

Credits

SNPsplit was written by Felix Krueger at Babraham Bioinformatics, now part of Altos Bioinformatics.