Release 0.4.0-alpha · luntergroup/octopus

This is a major release with important new features, enhancements, and performance improvements.

New features

New polyclone calling model for bacterial and viral data.
New population calling model with Hardy-Weinberg priors.
Random forest filtering for germline and somatic variants using ranger.
Generate an 'evidence' BAM for single sample calling with the --bamout option. See the wiki page for details.

The cancer caller can now model more than one somatic haplotype which improves calling sensitivity, and also allows somatic phasing. See cancer calling model wiki for more details.
Optimisation of the cancer model improves sensitivity for low frequency mutations.
New unified indel mutation model used for germline, de-novo, and somatic indel calling.
New filter Measures. See wiki for full list.
Tumour-only calling now much faster and more accurate.
Uses variant prior model to deduplicate haplotypes for all models, resulting in more biologically realistic calls.
DENOVO and SOMATIC calls now get different filtering treatment to regular germline variants using threshold filters.

Added --forest-file and --somatic-forest-file for random forest filtering.
Added --somatics-only to report only SOMATIC variants.
Added --denovos-only to report only DENOVO variants.
Added --max-somatic-haplotypes which limits the number of somatic haplotypes that may be used by the cancer calling model.
--consider-reads-with-unmapped-segments --> --no-reads-with-unmapped-segments and --consider-reads-with-distant-segments --> --no-reads-with-distant-segments. These filters are now off my default.
--max-cancer-genotypes removed and replaced with --max-genotypes, which is also used by the polyclone calling model.
Added --max-clones option for specifying the maximum number of clones for the polyclone calling model.
Added --somatic-filter-expression, --denovo-filter-expression, and --refcall-filter-expression which may be used for hard filtering 'DENOVO' and SOMATICcalls.