Bayesian haplotype-based mutation calling
This is a minor release with some bug fixes, and improvements to installation scripts.
cmake3 and cmake. Resolves #37. [30a3ffb11ad216e108efefcd70549130939655bb]This is a minor release that resolves a few issues in the first Beta release - v0.5.0-beta.
RFQUAL random forest score to the FORMAT field, so there is now one score for each sample. [81b75ea3af852e809c789a8a924b3aa0f9791264]RTB, REB, BMC, BMF. [f1000d4410fe62e8b0b8bd0080d4720b81024710, 1a937f2f48aad986ea76b799f666155da4fccc08]forest to the --training-annotations option (renamed from --csr-train). [519be06afbc7ddc3c70b4a5da899a22d18391b5c, 106e3443c4ed5319d84f621b5b0eaf50c46db179]--csr-train option to --training-annotations. [a1f8c45878ac1ca05c496f4b6b6c344c21a1ab10]RPB measure to RSB. [c52c6e8cb220e5db1171aa857141617b8aedf7c4]doubles are not parsed properly, causing errors when using random forest filtering. [dc137542403b7c9af73257151472936ccd5a0844]MQD measure. [45b9b742d09cb037ffa605c719695ae22d94a066]INFO and FORMAT fields with multiple values. [0078c5a1e2fbd1abd43a65315f4de216fbf4fa9b]This is the first beta release as most of the core features are reasonably mature. There have been various stability and runtime improvements, in addition to improvements to the core algorithm - including a completely new indel mutation model. Once again, the cancer calling model has received most attention, particularly for high depth ultra-low VAF tumour-only calling (e.g. UMI).
--repeat-candidate-generator command line option. [2856c2e6b8a5683f07c19d3f40e1c2f3b467bacd , 2856c2e6b8a5683f07c19d3f40e1c2f3b467bacd]QUAL is calculated in the cancer and trio models has been improved. Previously QUAL was the posterior probability the called alt allele segregated and is classified correctly. This could lead to low QUAL scores if the classification was uncertain (e.g. in tumour-only samples). QUAL is now simply the posterior probability the allele segregates. There is also a new annotation for all cancer caller calls, and DENOVO trio calls, PP, that is equivalent to the old QUAL. [905c96b7362ba2513c920e33d896751490cc32f0, 3b28e9fe85af4aef4408cb3b31c959408a0ba129, 0d1537b9012326d4e8e3d98d718e0f81ff73219e]SOMATIC have a new annotation: MAP_VAF which reports theMaximum a posteriori VAF estimate.VAF_CR) [e361f5065da83a9d1febabf4dcac9c7578dc3e8e].--max-vb-seeds which controls the maximum number of seeds the Variational Bayes based genotype model algorithms can use. [95c66a2ec89fe37adb8a4707d15b69bf17f25563]--split-bamout for split realigned BAMs. Split BAMs are no longer requested by specifying a prefix to --bamout. [34d8a89748cd363e967cea89774531efa73a9dbb]SC has been renamed to NC (Normal Contamination). [23497c3aaf0c93c9ca633f96778f8f74c4a5a4b3]
-- Adds --mask-tails for unconditionally masking bases of all read tails. [acfddaf1b5e910496b737f3dd6cab2667dadae4b]--tumour-germline-concentration which may be used to control shape of prior distribution on haplotype mixture frequency of tumour samples. Only really relevant to high depth tumour-only calling. [9f83ca6fce24ced6ea901845f3c474ecfc6a1867]--snv-denovo-mutation-rate to --denovo-snv-mutation-rate and --indel-denovo-mutation-rate to --denovo-indel-mutation-rate. [4b9d95f448ef1f8d2375947a58d664850a868c18]--repeat-candidate-generator to control new repeat candidate generator. [2856c2e6b8a5683f07c19d3f40e1c2f3b467bacd]configs directory in the main project directory that contains pre-written configs for calling certain types of data. [9da036416ff2bd7a36f5f734aebbd391df7c48f4]This is a major release with important new features, enhancements, and performance improvements.
--bamout option. See the wiki page for details.DENOVO and SOMATIC calls now get different filtering treatment to regular germline variants using threshold filters.--forest-file and --somatic-forest-file for random forest filtering.--somatics-only to report only SOMATIC variants.--denovos-only to report only DENOVO variants.--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.--max-clones option for specifying the maximum number of clones for the polyclone calling model.--somatic-filter-expression, --denovo-filter-expression, and --refcall-filter-expression which may be used for hard filtering 'DENOVO' and SOMATICcalls.This version brings new features, in addition to significant calling and runtime improvements.
--filter-vcf command line option).--threads command. This resolves #13.install.py is now supplied with both a C++ and C compiler with the cxx_compiler and c_compiler commands respectively.--no-supplementary-alignments changes to --allow-supplementary-alignments).--no-secondary-alignments changes to --allow-secondary-alignments).--clean with Python install script)..vcf.gz index files are now in the .tbi format, rather than .csi.This version brings bug fixes and some minor performance improvements.
This release contains some runtime performance improvements, particularly for the tumour calling model. It also updates the requirements for GCC, CMake, and Boost.
This is a major release that contains significant new features and improvements.
This release includes a new de novo mutation model that improves trio calling.
snv-denovo-mutation-rate and indel-denovo-mutation-rate. Gap open and extension penalties are weighted based on context.max-joint-genotypes to 1,000,00.