Updated documentation to reflect the changes made by swtiching over to the GRCm39 mouse genome, as well as the v8 annotation files. The v5 and v7 versions are probably no longer available for download, but we have left the option --v7 in there for backward compatibility for the time being.
- Updated the genome preparation to now work with the latest (v8) genome annotation file (mgp_REL2021_snps.vcf.gz) from the Mouse Genomes Project. The mgp_v5 version for the now outdated GRCm38 genome are now no longer supported (since this is primarily a screening tool anyway...).
- Added new option
--v7_VCFto 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
- Fixed an issue where allele-ratios were always assiged to the first strain in pairwise comparisons. Addressed in #2.
- Fixed the allele-ratio plot/table in the HTML report (it was picking these ratios in a rather random manner). Addressed in #1.
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Initial release. All basic tools seem to be working. Documentation and help need a little more work, but this will have to wait until after the holidays.
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Travis CI also needs some TLC (read: there are currently no use useful checks being carried out).