kevlar-dev/kevlar issues and pull requests

#388 - Is kevlar able to detect duplications/repeat expansions and in general CNV?

Issue - State: open - Opened by ashenflower over 3 years ago - 1 comment

#387 - Check number of controls

Pull Request - State: closed - Opened by standage over 3 years ago

#386 - > 30,000 variants reported from trio-analysis with FPR 0.001?

Issue - State: open - Opened by moldach about 4 years ago - 6 comments

#385 - count_control error: estimated false positive rate is 0.385 (FPR too high, bailing out!!!

Issue - State: open - Opened by moldach over 4 years ago - 5 comments

#384 - Kevlar novel multithreading

Issue - State: open - Opened by ghost over 4 years ago - 2 comments

#383 - How to just get the Kmer?

Issue - State: closed - Opened by ghost over 4 years ago

#382 - Where is kevlar?

Issue - State: closed - Opened by ghost over 4 years ago - 3 comments

#381 - VCF Parsing Issue

Issue - State: open - Opened by 17tranap over 4 years ago - 1 comment
Labels: bug

#380 - Controls for simlike

Issue - State: closed - Opened by 17tranap almost 5 years ago - 2 comments

#379 - partition, node error

Issue - State: closed - Opened by 17tranap almost 5 years ago - 4 comments

#378 - kevlar memory error

Issue - State: open - Opened by sph17 almost 5 years ago - 2 comments

#377 - Clarification - how to avoid high FPR

Issue - State: open - Opened by exeter-matthew-wakeling almost 5 years ago - 3 comments

#376 - Tutorial: Error on running kevlar filter

Issue - State: closed - Opened by exeter-matthew-wakeling almost 5 years ago - 9 comments

#375 - python 3.6 install - pytest failures - 26 failed, 347 passed (pytest 5.3.5?)

Issue - State: closed - Opened by blajoie about 5 years ago - 5 comments

#374 - Empty files produced by kevlar split cause crash of kevlar assemble

Issue - State: open - Opened by serosko about 5 years ago - 3 comments

#373 - Update exception handling

Pull Request - State: closed - Opened by standage about 5 years ago - 1 comment

#372 - Fix mock data download links

Pull Request - State: closed - Opened by standage about 5 years ago
Labels: documentation

#371 - Quick bugfixes

Pull Request - State: closed - Opened by standage about 5 years ago - 1 comment
Labels: bug

#370 - Dead links to tutorial files

Issue - State: closed - Opened by serosko about 5 years ago - 3 comments

#369 - Failed tests

Issue - State: closed - Opened by serosko over 5 years ago - 8 comments

#368 - Execution failed due to high FPR in case

Issue - State: closed - Opened by pkothiyal over 5 years ago - 4 comments

#367 - MemoryError

Issue - State: closed - Opened by mvelinder over 5 years ago - 3 comments

#366 - Implement max target length filter

Pull Request - State: closed - Opened by standage almost 6 years ago - 1 comment

#365 - A few fixes

Pull Request - State: closed - Opened by standage almost 6 years ago - 1 comment

#364 - Command or script for inspecting ambiguous calls

Issue - State: open - Opened by standage almost 6 years ago
Labels: enhancement

#363 - Dynamic error rate fix

Pull Request - State: closed - Opened by standage almost 6 years ago - 1 comment

#362 - Bug with log-space transformation

Issue - State: closed - Opened by standage almost 6 years ago
Labels: bug, accuracy

#361 - Ambiguous contig threshold

Pull Request - State: closed - Opened by standage almost 6 years ago - 1 comment

#360 - Filter for contigs with ambiguous calls

Issue - State: closed - Opened by standage almost 6 years ago
Labels: enhancement, accuracy

#359 - Update VCF parser

Pull Request - State: closed - Opened by standage almost 6 years ago - 2 comments
Labels: bug, enhancement

#358 - Issues parsing scalpel VCF

Issue - State: closed - Opened by standage almost 6 years ago
Labels: bug

#357 - Update the documentation

Pull Request - State: closed - Opened by standage almost 6 years ago - 1 comment
Labels: enhancement, documentation

#356 - Analysis notebooks

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment

#355 - Add varfilter to mark-I workflow

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment

#354 - Reimplement varfilter module

Pull Request - State: closed - Opened by standage about 6 years ago - 2 comments
Labels: refactoring, optimization

#353 - Drop all handling of mate sequences

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: refactoring

#352 - Recompile extensions using latest version of Cython

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment

#351 - Update to variant.annotate

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment

#350 - New filter to drop high abundance outlier k-mers

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: accuracy

#349 - Poor likelihood score when terminal spanning k-mers have high abundance

Issue - State: closed - Opened by standage about 6 years ago
Labels: accuracy

#348 - Kevlar simlike --refr flag required

Issue - State: closed - Opened by standage about 6 years ago
Labels: bug

#347 - "Replace" option for variant.annotate method

Issue - State: closed - Opened by standage about 6 years ago
Labels: bug

#346 - Clean up get_abundances function

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: refactoring

#345 - Reimplement varfilter

Issue - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: refactoring, optimization

#344 - Revisit matedist filter

Issue - State: closed - Opened by standage about 6 years ago
Labels: refactoring

#343 - New --min-like-score filter for simlike module

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: enhancement, accuracy

#342 - Save and load pickled varfilter index

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: optimization

#341 - Option to adjust LIKESCORE cutoff

Issue - State: closed - Opened by standage about 6 years ago
Labels: accuracy

#340 - Option to store and load pickle of interval forest in varfilter module

Issue - State: closed - Opened by standage about 6 years ago
Labels: enhancement, optimization

#339 - Filter based on proband k-mer abundance

Pull Request - State: closed - Opened by standage about 6 years ago - 2 comments
Labels: accuracy

#338 - Update to homopolymer filter

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: accuracy

#337 - Fix bug with merging variants

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: bug

#336 - Filter short indels abutting homopolymers

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: accuracy

#335 - Sandbox scripts

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: enhancement

#334 - Utility scripts

Issue - State: closed - Opened by standage about 6 years ago

#333 - Homopolymer filter

Issue - State: closed - Opened by standage about 6 years ago
Labels: accuracy

#332 - Handle multinucleotide variants correctly

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: bug, accuracy

#331 - Adjacent SNVs (multinucleotide variants) called incorrectly

Issue - State: closed - Opened by standage about 6 years ago
Labels: bug, accuracy

#330 - Clean up `get_abundances` function

Issue - State: closed - Opened by standage about 6 years ago

#329 - Bring varfilter into Snakemake workflow

Issue - State: closed - Opened by standage about 6 years ago
Labels: enhancement

#328 - Speed up simlike by skipping calculations for filtered variants

Pull Request - State: closed - Opened by standage about 6 years ago - 2 comments
Labels: optimization

#327 - Introduce --ctrl-max heurisitic at simlike stage

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: accuracy

#326 - Dynamically compute length of output for functional test

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: enhancement

#325 - Normalize likelihood scores by number of spanning k-mers

Issue - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: wontfix

#324 - Skip likelihood score calculation for some filtered calls

Issue - State: closed - Opened by standage about 6 years ago
Labels: optimization

#323 - Investigate --ctrl-max as a heuristic when calculating likelihood score

Issue - State: closed - Opened by standage about 6 years ago
Labels: accuracy

#322 - Update filter command in workflow Mark I

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: bug

#321 - Logging updates

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: enhancement

#320 - Update workflow Mark I to match updates to filter module

Issue - State: closed - Opened by standage about 6 years ago
Labels: bug

#319 - The state of the log

Issue - State: closed - Opened by standage about 6 years ago
Labels: enhancement

#318 - New "varfilter" module

Pull Request - State: closed - Opened by standage about 6 years ago
Labels: enhancement, accuracy

#317 - Window check bugfix

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: bug

#316 - Split filter module functionality

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment

#315 - Split out functionality of filter module

Issue - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: refactoring, optimization

#314 - Split workflow

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: optimization

#313 - Simlike bug fix for short reference window

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: bug

#312 - Minor updates to workflow Mark I

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: bug

#311 - Check size of reference window in simlike

Issue - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: bug

#310 - Put `--include` parameter value in single quotes in workflow Mark I

Issue - State: closed - Opened by standage about 6 years ago
Labels: bug

#309 - Fix logging in assembly module

Issue - State: closed - Opened by standage about 6 years ago
Labels: bug

#308 - Huge update to logging code

Pull Request - State: closed - Opened by standage about 6 years ago - 2 comments
Labels: refactoring, documentation

#307 - Refactor logging code

Issue - State: closed - Opened by standage about 6 years ago
Labels: refactoring, documentation

#306 - New workflow (mark I)

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: configuration

#305 - New workflow for preprocessing BAM data

Pull Request - State: closed - Opened by standage about 6 years ago - 2 comments
Labels: enhancement, documentation

#304 - Fix erroneous contig attribute with indels

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: bug

#303 - Discard short alignment blocks prior to variant calling

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: enhancement, accuracy

#302 - Extend variant-spanning-kmer-mask capability to `kevlar call`

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: enhancement

#301 - Updates to localize & alac modules

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: enhancement, refactoring, optimization

#300 - Updates to documentation

Pull Request - State: closed - Opened by standage about 6 years ago - 1 comment
Labels: documentation

#297 - Things to deprecate

Issue - State: closed - Opened by standage about 6 years ago
Labels: enhancement

#296 - Update docs

Issue - State: closed - Opened by standage about 6 years ago
Labels: documentation

#295 - Add --gen-mask flag to `kevlar call`

Issue - State: closed - Opened by standage about 6 years ago
Labels: enhancement

#293 - [WIP] Fix erroneously filtered indel call

Pull Request - State: closed - Opened by standage over 6 years ago - 2 comments
Labels: bug, accuracy

#284 - Un-pin pytest version

Issue - State: closed - Opened by standage over 6 years ago - 1 comment

#282 - error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'

Issue - State: closed - Opened by tseemann over 6 years ago - 3 comments

#260 - Investigate variants with short spanning windows

Issue - State: closed - Opened by standage over 6 years ago - 2 comments

#252 - Idea: drop partitions where all calls have MD=inf

Issue - State: closed - Opened by standage almost 7 years ago
Labels: accuracy

#176 - Publish "nobel" trios

Issue - State: closed - Opened by standage about 7 years ago

#175 - Evaluate performance on "nobel" trios

Issue - State: closed - Opened by standage about 7 years ago
Labels: accuracy

#61 - Report kevlar version when running a script

Issue - State: open - Opened by standage almost 8 years ago - 3 comments

GitHub / kevlar-dev/kevlar issues and pull requests