Bayesian haplotype-based mutation calling
QUAL
scores less than 1
are now reported to 2 significant figures.This release contains several minor improvements:
--disable-call-filtering
is used. To aggregate annotations for forest training, the --aggregate-annotations
option is added. [42f424870307861e6eb9cb8f53245f03357973f6]cell
calling model. [bc062d24c1e344a09ba42240e206f604ad8ab771]--max-genotype-combinations
to 100,000
for trio
and population
calling. This improves runtime considerably but has little impact on accuracy. [18fcbcbc354479ebf0abe6a2d08e048041eb0918]This is a minor bug fix release:
--annotations
specified with --help
. [366fe044327504487e50f51224582e82d3fdda1e]This is a minor bug fix release:
AD
) on *
alleles [e0023adf0f1bf0f97af474a0a5016ea213f1cc62].--architecture
option to install.py
that sets compiler march
option [87faea93b08e465c74dd28c7452a66a74a644ed2].This is a major release since v0.6.3-beta
and is the first non-beta
release. Highlights include:
--read-linkage
option. This improves accuracy and phasing for most analysis.AD
) are now supported; they can be requested with the --annotations
option.--backtrack-level
option.QUAL
and GQ
have been reduced allowing for much greater ranges on these statistics.*
ALT
allele has been brought inline with the updated VCF v4.3 specification. The --legacy
option has therefore been removed.RFGQ_ALL
INFO
measure for random forest filtered runs - the empirical probability (Phred) of all genotypes being correct (derived from each FORMAT
RFGQ
). Use this for filtering tumour-normal calls etc.--max-genotypes
option is used (recommended for anything over triploid).--allow-cycles
option.GT
entires) are now reported in a consistent manner - always lexicographical (w.r.t the implied haplotype). This breaks the previous rule that somatic haplotypes always appeared after germline ones - somatic haplotypes are now identified with the HSS
FORMAT
annotation.This release reduces runtime in the cancer
and polyclone
calling models by 20-25%; fixes a bug in the read deduplication algorithm, resulting in fewer false positive calls in PCR data (particularly for somatic calling), adds new read pre-processing options designed to mitigate systematic artefacts in 10X Genomics sequencing, and adds a new way to metric (RFQUAL_ALL
) to filter somatic variant calls.
--mask-inverted-soft-clipping
and --mask-3prime-shifted-soft-clipped-heads
for masking 10X Genomics sequencing artefacts. [0b8fb935d93154b624f644940e0375f8c92b62c0, 6566fb2432cdac01fa43e0b217ae985c105993e9]VariationalBayesMixtureMixtureModel
used in the cancer
and polyclone
calling models by ~20-25% [d9cbcec3c24a9460d709b30ff0ea006d08e55491]cancer
calling model to use GMP library, resulting in a small speedup. This change adds a dependency to GMP. [e59be9dbf5cd768846b3de1170a185d67d3a06d3]NC
and SMQ
measures that could cause an exception to be thrown. [a1262e2a14d6c2efa7c7045a470cfe4b3dd7a209, 226b40a272cbd57721c29645b882637ac15474ef]This is a minor bug fix release.
This is a minor release that fixes some bugs, compilation issues, and adds better binary version logging.
--version
command. [242dd00549cc27f6629619d5d3bf7c0866ff0c29, 36a6a82c28d99cd17f0e169fa28e876f28b0c82f, c6c397d1ca5d3c50a372c83d6a75ca491ef4e678]ADP
for assigned sequence depth (i.e. reads assigned to a unique called allele). [702109ee85f362c6cce739aa0ff3a1be19e436a8]ADP
and VL
to default random forest measures. [a0359530077794cadb3723253f5fb783d9fca975]--regions-file
and --skip-regions-file
) [ec41af47350067808c3c27a434563a948bf652dc]AD
and AF
calculations. [2a6a1065319a4cb0416f2162def18b362d9e09d2 , 66e4466350edb5c7c17c2eab218e46f28699293b]This release improves calling accuracy, includes more flexible error modelling, and adds annotations to filtered VCF and realigned BAM files.
--training-annotations
option is replaced with --annotations
, with has slightly different behaviour (see below).--split-bamout
option is removed as --bamout
realignments now include tags.--full-bamout
. [1147e8f72f0fe3613ace63580ee592677f2f8466]--refcall-block-merge-threshold
for controlling recall blocks.--extract-filtered-source-candidates
to --use-filtered-source-candidates
. [6972ffaf0f5ca88fb56e2b5e5f7a066462f64a37]--annotations
option. [c75cbac60cdc27864b29097f1d608d89d31cbb68]--refcall-block-merge-threshold
option. [9127cf3f6f5a11f0268e14b9e51f177b9d1825d3]This is a minor release containing some bug fixes and an improved installation method.
--download
to --download-forests
in Python installation script. [166b6bea998242a821a23074f04253266976d297]--temp-directory-prefix
for setting name of temporary directory. [69ea9e73c41b73ffd6f93d9c1df9ba13588d21de]cell
caller prototype (undocumented). [9f496d30e01e12146e5face4a010f42ee0407c23]:
(e.g. HLA-A*01:01:01:01). Resolves #44. [https://github.com/luntergroup/octopus/commit/37a3329239518a07b2b9ca62e28a7570d9773667]