MGP v8 annotations and GRCm39

Switched over to the GRCm39 mouse genome build, as well as the v8 annotation file. The v5 and v7 versions are probably no longer available for download from Ensembl, but we have left the option --v7 in there for backward compatibility for the time being.

The documentation and genome preparation do now work with the latest genome annotation file (v8, mgp_REL2021_snps.vcf.gz) from the Mouse Genomes Project.

v0.3.0 - v7 SNP VCF support

reStraining

• Added new option --v7_VCF to allow using the file 'mgp_REL2005_snps_indels.vcf.gz' instead of the mgp.v5 file mentioned in the main documentation. This file contains both SNP and INDEL information, but INDELs are skipped. The mgp.v5 file is still listed as Current_SNPs, so the v7 file is still considered experimental. The v7 file contains a number of additional strains, and was released in May2020. Get it here: ftp://ftp-mouse.sanger.ac.uk/REL-2004-v7-SNPs_Indels/mgp_REL2005_snps_indels.vcf.gz

reStrainingOrder

• Fixed an issue where allele-ratios were always assiged to the first strain in pairwise comparisons. Addressed in #2.

0.2.0

reStrainingOrder v0.2.0

• HTML report does now show the correct allele-ratios for potential hybrid strains (see #1 for details).

0.1.0 - Initital Release

This is the first public release of reStrainingOrder. The tool is working in our hands using the sample commands described in the User Guide.

We are aware that there is still some work to do regarding documentation (help text), tidying up the code, and potentially improving the runtime or memory consumption. Nevertheless, please give it a whirl and let us know if you have any comments or suggestions!