NVIDIA VariantWorks issues

NVIDIA / VariantWorks

Deep Learning based variant calling toolkit - https://clara-parabricks.github.io/VariantWorks/

Apache License 2.0

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issues

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Bump nemo-toolkit from 0.10.1 to 1.6.0

#171 dependabot[bot] opened 2 years ago
0
Bump numpy from 1.18.3 to 1.22.0

#170 dependabot[bot] opened 2 years ago
1
simple_consensus_caller , how to automatically remove

#169 jelber2 opened 2 years ago
0
Relu

#168 avantikalal closed 3 years ago
0
Apply softmax to the model only during inference

#167 ohadmo closed 3 years ago
0
VariantWorks simple_consensus _caller does not go to zero training loss / perfect training accuracy when expected

#166 michaelbrownid closed 3 years ago
3
Modified cnn

#165 avantikalal closed 3 years ago
0
[encoder] fix bug in adding ref info to summary encoding

#164 tijyojwad closed 3 years ago
2
[dataloader] improve hdf data loader

#163 tijyojwad closed 3 years ago
0
Added Consensus CNN

#162 rahulmohan opened 3 years ago
0
[consensus] add multi gpu training docs to consensus sample

#161 tijyojwad closed 3 years ago
0
[encoding] update encoding to add draft base and base quality

#160 tijyojwad closed 3 years ago
0
[sample] filtering to consensus sample

#159 tijyojwad opened 3 years ago
0
[loss] focal loss throwing an error when used in place of ce loss

#158 tijyojwad opened 3 years ago
0
Added attention consensus model

#157 rahulmohan opened 3 years ago
0
[Encoders] Handle exception `samtools mpileup` output when searching for insertions in SummaryEncoder

#156 ohadmo opened 3 years ago
0
Add tabix index file input option, catch invalid format error

#155 ntadimeti closed 3 years ago
0
Add input BAM files support to simple consensus caller sample

#154 ohadmo closed 3 years ago
0
Brass BEDPE

#153 mp15 closed 3 years ago
1
BED/BEDPE Overwrite rather than create new typed columns + offbyone fix

#152 mp15 closed 3 years ago
2
Adapt FastxWriter to support more arguments

#151 ohadmo closed 3 years ago
1
[I/O] KeyErrors are thrown for info columns not present in a region

#150 edawson opened 3 years ago
1
[consensus_caller] fix categorical accuracy calculation

#149 tijyojwad closed 3 years ago
1
[CI] Add nightly wheel package versioning

#148 ohadmo closed 3 years ago
0
Support FASTA output format in FastxWriter class

#147 ohadmo closed 3 years ago
1
[ci] fix CPU CI tests

#146 tijyojwad closed 3 years ago
0
[io] add generic parser for BED files

#145 tijyojwad closed 3 years ago
2
Feature request: BEDPE format for ingesting SV data

#144 mp15 closed 3 years ago
8
[CI] Add full CI support- Auto-release & nightly builds

#143 ohadmo closed 3 years ago
0
MultiZMW stitching, model structure inputs, log(0) fixes

#142 michaelbrownid closed 3 years ago
13
VCFReader re-implemented with pysam

#141 ntadimeti closed 3 years ago
2
New focal loss

#140 rahulmohan closed 3 years ago
0
Add alternative setup instructions through Anaconda

#139 ohadmo closed 3 years ago
1
[sample] add new sample with scalar vcf values

#138 tijyojwad opened 4 years ago
0
[model] add optional softmax layer to consensus rnn

#137 tijyojwad closed 4 years ago
1
simple_consensus_caller sample fails with negative probabilites.

#136 michaelbrownid closed 3 years ago
4
[I/O] Update VCF -> cuDF parser with more optimized version

#135 tijyojwad opened 4 years ago
0
Removed softmax from RNN forward pass

#134 rahulmohan closed 4 years ago
0
Add quality score output for the consensus pipeline

#133 ohadmo closed 4 years ago
0
[encoder] support latest samtools mpileup for summary encoder

#132 tijyojwad opened 4 years ago
0
[model] add quality score output for consensus pipeline

#131 tijyojwad closed 4 years ago
0
[loss] add focal loss support

#130 tijyojwad closed 3 years ago
0
[I/O] VCFReader crashes when reading from regions that are empty

#129 edawson opened 4 years ago
0
[samples] add inference sample for simple snp trainer

#128 ohadmo opened 4 years ago
0
Added Focal Loss

#127 rahulmohan closed 4 years ago
1
[IO] fix multi gpu data loading

#126 tijyojwad closed 4 years ago
0
[docs] update docs to showcase new features

#125 tijyojwad closed 4 years ago
0
[visualization] ReadPileup visualizer to take encoding as input

#124 tijyojwad opened 4 years ago
0
[I/O] HDF Data Loader not showing speedup for multi threaded

#123 tijyojwad opened 4 years ago
1
[consensus sample] add README and sample data

#122 tijyojwad closed 4 years ago
0