kevlar-dev kevlar issues

kevlar-dev / kevlar

Reference-free variant discovery in large eukaryotic genomes

https://kevlar.readthedocs.io

MIT License

40 stars 9 forks source link

issues

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

#388 ashenflower opened 2 years ago
1
Check number of controls

#387 standage closed 3 years ago
0
> 30,000 variants reported from trio-analysis with FPR 0.001?

#386 moldach opened 3 years ago
6
count_control error: estimated false positive rate is 0.385 (FPR too high, bailing out!!!

#385 moldach opened 3 years ago
5
Kevlar novel multithreading

#384 ghost opened 4 years ago
2
How to just get the Kmer?

#383 ghost closed 4 years ago
0
Where is kevlar?

#382 ghost closed 4 years ago
3
VCF Parsing Issue

#381 17tranap opened 4 years ago
1
Controls for simlike

#380 17tranap closed 4 years ago
2
partition, node error

#379 17tranap closed 4 years ago
4
kevlar memory error

#378 sph17 opened 4 years ago
2
Clarification - how to avoid high FPR

#377 exeter-matthew-wakeling opened 4 years ago
3
Tutorial: Error on running kevlar filter

#376 exeter-matthew-wakeling closed 4 years ago
9
python 3.6 install - pytest failures - 26 failed, 347 passed (pytest 5.3.5?)

#375 blajoie closed 4 years ago
5
Empty files produced by kevlar split cause crash of kevlar assemble

#374 serosko opened 4 years ago
3
Update exception handling

#373 standage closed 4 years ago
1
Fix mock data download links

#372 standage closed 4 years ago
0
Quick bugfixes

#371 standage closed 4 years ago
1
Dead links to tutorial files

#370 serosko closed 4 years ago
3
Failed tests

#369 serosko closed 4 years ago
8
Execution failed due to high FPR in case

#368 pkothiyal closed 4 years ago
4
MemoryError

#367 mvelinder closed 4 years ago
3
Implement max target length filter

#366 standage closed 5 years ago
1
A few fixes

#365 standage closed 5 years ago
1
Command or script for inspecting ambiguous calls

#364 standage opened 5 years ago
0
Dynamic error rate fix

#363 standage closed 5 years ago
1
Bug with log-space transformation

#362 standage closed 5 years ago
0
Ambiguous contig threshold

#361 standage closed 5 years ago
1
Filter for contigs with ambiguous calls

#360 standage closed 5 years ago
0
Update VCF parser

#359 standage closed 5 years ago
2
Issues parsing scalpel VCF

#358 standage closed 5 years ago
0
Update the documentation

#357 standage closed 5 years ago
1
Analysis notebooks

#356 standage closed 5 years ago
1
Add varfilter to mark-I workflow

#355 standage closed 5 years ago
1
Reimplement varfilter module

#354 standage closed 5 years ago
2
Drop all handling of mate sequences

#353 standage closed 5 years ago
1
Recompile extensions using latest version of Cython

#352 standage closed 5 years ago
1
Update to variant.annotate

#351 standage closed 5 years ago
1
New filter to drop high abundance outlier k-mers

#350 standage closed 5 years ago
1
Poor likelihood score when terminal spanning k-mers have high abundance

#349 standage closed 5 years ago
0
Kevlar simlike --refr flag required

#348 standage closed 5 years ago
0
"Replace" option for variant.annotate method

#347 standage closed 5 years ago
0
Clean up get_abundances function

#346 standage closed 5 years ago
1
Reimplement varfilter

#345 standage closed 5 years ago
1
Revisit matedist filter

#344 standage closed 5 years ago
0
New --min-like-score filter for simlike module

#343 standage closed 5 years ago
1
Save and load pickled varfilter index

#342 standage closed 5 years ago
1
Option to adjust LIKESCORE cutoff

#341 standage closed 5 years ago
0
Option to store and load pickle of interval forest in varfilter module

#340 standage closed 5 years ago
0
Filter based on proband k-mer abundance

#339 standage closed 5 years ago
2