Illumina/SpliceAI issues and pull requests

#155 - I failed to reproduce SpliceAI training based on the source code.

Issue - State: open - Opened by shiro-kur 10 days ago - 5 comments

#155 - I failed to reproduce SpliceAI training based on the source code.

Issue - State: open - Opened by shiro-kur 10 days ago - 5 comments

#154 - Variant present in SpliceAI lookup absent in spliceai_scores.masked.snv.hg19.vcf.gz

Issue - State: open - Opened by Roshanshafiha 13 days ago - 4 comments

#153 - Help with scoring custom sequence

Issue - State: open - Opened by albustruong about 1 month ago

#152 - Mask not computed correctly. Possible off-by-1 error?

Issue - State: open - Opened by bw2 3 months ago - 1 comment

#151 - No training configuration found in save file

Issue - State: open - Opened by YS-Github-bug 5 months ago - 1 comment

#150 - Delta positon score interpretation for deletions.

Issue - State: open - Opened by drjraclarke 6 months ago

#149 - Figure 1c Reproduction

Issue - State: open - Opened by prakruthiburra 7 months ago - 3 comments

#148 - Way to many TEMP files

Issue - State: open - Opened by ttys42 7 months ago

#147 - WARNING:root:Skipping record (ref too long)

Issue - State: open - Opened by Zer0day-0 7 months ago

#146 - Query about spliceai to calculate Delins

Issue - State: closed - Opened by HXD3D0323 10 months ago - 1 comment

#145 - spliceai score

Issue - State: open - Opened by jml96 12 months ago - 3 comments

#144 - No training configuration found in the save file, so the model was not compiled. Compile it manually.

Issue - State: closed - Opened by Ritetsu about 1 year ago - 3 comments

#143 - How to make a custom annotation set?

Issue - State: open - Opened by dudududu12138 about 1 year ago - 2 comments

#142 - build-in grch38 annotation

Issue - State: open - Opened by yanwang271 about 1 year ago

#141 - Running Short Tandem Repeat genotypes

Issue - State: open - Opened by Nehir291 over 1 year ago

#140 - Unable to install using conda install

Issue - State: open - Opened by rodrigodealexandre over 1 year ago - 1 comment

#139 - Duplicate records in the released VCF file

Issue - State: open - Opened by lacek over 1 year ago - 3 comments

#138 - Running SpliceAI takes too much time

Issue - State: open - Opened by gswsqffsapd3056 over 1 year ago - 1 comment

#137 - variant not scored

Issue - State: open - Opened by carolinehey over 1 year ago - 5 comments

#136 - Question about using snv and indel score files

Issue - State: open - Opened by cgy0627 over 1 year ago

#135 - Training input shape

Issue - State: closed - Opened by carmelle-cat over 1 year ago - 1 comment

#134 - Position of splice sites within an insertion

Issue - State: closed - Opened by baumanale over 1 year ago - 1 comment

#133 - spliceAI not giving output value while running using vep (Variant Ensemble Predictor)

Issue - State: closed - Opened by sruthisrini over 1 year ago - 3 comments

#132 - Trouble to launch SpliceAI with grch37

Issue - State: closed - Opened by JbaptisteLam over 1 year ago - 5 comments

#131 - Training with additional Batch Normalization layer producing strange results

Issue - State: closed - Opened by immanuelazn over 1 year ago - 1 comment

#130 - Lower Accuracy Than Introme

Issue - State: closed - Opened by DarioS over 1 year ago - 1 comment

#129 - Interpret SpliceAI result

Issue - State: closed - Opened by sophienguyen01 over 1 year ago

#128 - Delta position seems to be wrong for this variant

Issue - State: closed - Opened by Manuel-DominguezCBG over 1 year ago - 1 comment

#127 - Transcript Dependent Scores

Issue - State: closed - Opened by officedronestrike over 1 year ago - 1 comment

#126 - cryptic splice sites

Issue - State: closed - Opened by prasundutta87 over 1 year ago - 2 comments

#125 - Delta score interpretation

Issue - State: closed - Opened by yanwang271 over 1 year ago - 1 comment

#124 - How to interpret Delta position in insertion/deletion variants

Issue - State: closed - Opened by Manuel-DominguezCBG over 1 year ago - 2 comments

#123 - query about spliceAI score generation used as input file in VEP

Issue - State: closed - Opened by prasundutta87 over 1 year ago - 1 comment

#122 - syntax error

Issue - State: closed - Opened by cycan8130 almost 2 years ago - 1 comment

#121 - Which annotations are used in the published paper?

Issue - State: closed - Opened by exnx almost 2 years ago - 1 comment

#120 - how to annotate just one gene

Issue - State: closed - Opened by agomez700 almost 2 years ago - 1 comment

#119 - Added support and testing for MNPs

Pull Request - State: open - Opened by kdahlo almost 2 years ago - 4 comments

#118 - TypeError: slice indices must be integers or None or have an index method

Issue - State: closed - Opened by MangGuoBingqilin almost 2 years ago - 6 comments

#117 - pysam errors

Issue - State: closed - Opened by cycan8130 almost 2 years ago

#116 - zsh: command not found: spliceai

Issue - State: closed - Opened by cycan8130 almost 2 years ago - 4 comments

#115 - spliceai_scores.masked.indel.hg19.vcf.gz DL never ends

Issue - State: closed - Opened by PBMCHUGA almost 2 years ago - 2 comments

#114 - ImportError: cannot import name 'Literal' from 'typing'

Issue - State: closed - Opened by udp3f about 2 years ago - 2 comments

#113 - spliceAI_score vcf

Issue - State: closed - Opened by forrestzhaosen about 2 years ago - 4 comments

#112 - TET2: Why is the module returning only one value, which doesn’t appear to match the canonical transcript.

Issue - State: closed - Opened by cpsosa0006 about 2 years ago - 1 comment

#111 - downloading from basespace?

Issue - State: closed - Opened by pauline-ng about 2 years ago - 1 comment

#110 - Scoring splicing probability of novel splice sites

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

#109 - Upgrade Libraries and deal with multi-nucleotide polymorphisms (MNP)

Issue - State: open - Opened by sicotteh over 2 years ago

#108 - How to increase calculation speed

Issue - State: closed - Opened by MattCloward over 2 years ago - 1 comment

#107 - Why do i got two results for one postion?

Issue - State: closed - Opened by genegogo2019 over 2 years ago - 2 comments

#106 - Attribute error: module 'tensorflow.python.util.dispatch' has no attribute 'add_fallback_dispatch_list'

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

#105 - Working with genes on - strand

Issue - State: closed - Opened by Abhinav-Mittal over 2 years ago - 1 comment

#104 - SpliceAI scores pre-calculation with in silico mutagenesis

Issue - State: closed - Opened by SIJAE-WOO almost 3 years ago - 1 comment

#103 - Score for some mutations in Illumina files make zero biological sense

Issue - State: closed - Opened by BJWiley233 almost 3 years ago - 3 comments

#102 - dual variants

Issue - State: closed - Opened by zyh4482 almost 3 years ago - 1 comment

#101 - output missing for some variants

Issue - State: closed - Opened by mvheetve almost 3 years ago - 1 comment

#100 - Documentation improvement (Suggestion)

Issue - State: closed - Opened by jpuntomarcos almost 3 years ago - 1 comment

#99 - Scores generated by newer GPUs are very odd.

Issue - State: open - Opened by Luobiny almost 3 years ago - 5 comments

#98 - Test datasets including variants info

Issue - State: closed - Opened by SIJAE-WOO about 3 years ago - 1 comment

#97 - NameError: name 'CVM' is not defined

Issue - State: closed - Opened by KunFang93 about 3 years ago - 4 comments

#96 - hg19/hg38

Issue - State: closed - Opened by AGunnell77 about 3 years ago - 2 comments

#95 - AttributeError: 'str' object has not attribute 'decode'

Issue - State: closed - Opened by AGunnell77 about 3 years ago - 6 comments

#94 - SpliceAI Batching Support

Pull Request - State: open - Opened by kazmiekr about 3 years ago - 2 comments

#93 - limit the CPU of SpliceAI?

Issue - State: closed - Opened by zofieLin about 3 years ago - 1 comment

#92 - Updated SpliceAI toolset to output raw scores in VCF

Pull Request - State: open - Opened by h-joshi about 3 years ago - 1 comment

#91 - TypeError: Parameter to MergeFrom() must be instance of same class

Issue - State: closed - Opened by bwubb about 3 years ago - 1 comment

#90 - Annotation-free predictions?

Issue - State: closed - Opened by Hoeze about 3 years ago - 1 comment

#89 - Performance GTEx model

Issue - State: closed - Opened by tabeariepe about 3 years ago - 2 comments

#88 - No training config

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

#87 - How is the principal transcript determined in the training dataset?

Issue - State: closed - Opened by erwinerdem over 3 years ago - 2 comments

#86 - Switch to interval tree

Pull Request - State: closed - Opened by NatPRoach over 3 years ago - 1 comment

#85 - Which training dataset was used for PyPI SpliceAI model?

Issue - State: closed - Opened by shiro-kur over 3 years ago - 2 comments

#84 - Fail to reproduce the result of fig 1e in the paper

Issue - State: closed - Opened by YuhaoTan2 over 3 years ago - 10 comments

#83 - Implementaion of SpliceAI without a input VCF

Issue - State: closed - Opened by wigge206 over 3 years ago - 1 comment

#82 - Fail to train the spliceai model with tensorflow 2.1.0

Issue - State: closed - Opened by YuhaoTan2 over 3 years ago - 2 comments

#81 - Attribute error

Issue - State: closed - Opened by nikigogate over 3 years ago - 9 comments

#80 - Installing with pip 21.2.3 results in ImportErrors

Issue - State: closed - Opened by jwhite3 over 3 years ago - 1 comment

#79 - Sequence-to-Sequence Mode

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

#78 - How to leverage a GPU to speed up SpliceAI

Issue - State: closed - Opened by nh13 over 3 years ago - 3 comments

#77 - indel or snv problem.

Issue - State: closed - Opened by summerghw over 3 years ago - 1 comment

#76 - Coverting probability to delta score

Issue - State: closed - Opened by wososa over 3 years ago - 15 comments

#75 - Different results between SpliceAI 1.3.1 on cluster versus Broad web version

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

#74 - Distance to event

Issue - State: closed - Opened by angelolimeta over 3 years ago - 1 comment

#73 - Installing issue; Solving environment: failed with initial frozen solve. Retrying with flexible solve.

Issue - State: closed - Opened by tsykit almost 4 years ago

#72 - IndexError: list index out of range

Issue - State: closed - Opened by gopi1616 almost 4 years ago - 1 comment

#71 - Input data and Tensorflow version2

Issue - State: closed - Opened by SIJAE-WOO almost 4 years ago - 8 comments

#70 - VCF file with ExAC variants tested?

Issue - State: closed - Opened by joycekang about 4 years ago - 1 comment

#69 - Getting SpliceAI annotations per bp in an input sequence (where output would be probability over donor/acceptor/neither)

Issue - State: closed - Opened by joycekang about 4 years ago - 4 comments

#68 - ImportError libcrypto.so.1.0.0 (via conda)

Issue - State: closed - Opened by Jjuj66 about 4 years ago - 2 comments

#67 - Running custom sequence doesn't produce an output

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

#66 - One-Based Vs Zero-Based Coordinate Systems

Issue - State: closed - Opened by CarlosBorroto about 4 years ago - 4 comments

#65 - Adding support for a GFF annotator.

Pull Request - State: closed - Opened by CarlosBorroto about 4 years ago - 1 comment

GitHub / Illumina/SpliceAI issues and pull requests