bioinform somaticseq issues

bioinform / somaticseq

An ensemble approach to accurately detect somatic mutations using SomaticSeq

http://bioinform.github.io/somaticseq/

BSD 2-Clause "Simplified" License

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issues

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makeSomaticScripts.py "single" generated command incorrectly passes vcf.gz file to option -d of lofreq call.

#134 harrymatthews50 closed 3 days ago
2
snakemake implementation support tumour-only samples.

#133 harrymatthews50 opened 1 week ago
1
ntree_limit deprecated into iteration_range in xgboost>=1.4

#132 litaifang closed 5 months ago
0
AI consensus calling error on WGS samples

#131 GACGAMA opened 5 months ago
9
Error when running FFPE training data from SEQ2C

#130 GACGAMA closed 5 months ago
5
Are multi-nucleotide and complex variants ignored?

#129 rebber opened 5 months ago
2
how to obtain all variants where the "FILTER" column is not labeled as "PASS"

#128 xiechangxiao closed 7 months ago
1
UnboundLocalError: cannot access local variable 'normal_name' where it is not associated with a value

#127 SAADAT-Abu closed 5 months ago
10
Output allele of the normal sample

#126 fredsamhaak opened 10 months ago
2
Error when running makeSomaticScripts with multiple threads

#125 GACGAMA closed 10 months ago
3
Dockerized alignment workflow does not work with multiple input files

#124 GACGAMA closed 11 months ago
5
Applying internal filters to outputs before running SomaticSeq

#123 ronkesm closed 5 months ago
1
somaticseq failing for same command it had previously successfully run

#122 csreej27 closed 5 months ago
11
Ground Truths required for training

#121 harish0201 closed 1 year ago
1
Where are the 10x Genomics single-cell copy number variation (CNV) analysis results?

#120 genetronhealth closed 1 year ago
7
Question for the paper on establishing the reference call set

#119 FriederikeHanssen closed 1 year ago
3
Slow RNA variant calling

#118 katjur01 opened 1 year ago
8
Somaticseq makeSomaticScripts.py running and output issues

#117 csreej27 closed 1 year ago
8
SEQC2: Some high confidence SNVs and INDELs in VCF are outside of regions defined by High-Confidence_Regions_v1.2.bed

#116 luederm closed 1 year ago
2
Docker issue with latest version

#115 emucaki closed 1 year ago
1
Pretrained Classifier

#114 kokyriakidis closed 1 year ago
3
Question about simulating somatic mutations

#113 leedchou closed 1 year ago
7
Special setting for b37?

#112 yoda0612 closed 2 years ago
14
Result of TNscope caller

#111 yoda0612 closed 2 years ago
4
Filter truth vcf files for dbsnp?

#110 iserf closed 2 years ago
1
somatic_xgboost.py train: xgboost.core.XGBoostError

#109 iserf closed 2 years ago
0
SV truthset for SEQC

#108 miyakokodama closed 2 years ago
1
makeSomaticScripts.py single mode passing certain arguments

#107 dnousome closed 2 years ago
2
generating training data using single medium-coverage replicate of normal sample

#106 kiranchari closed 2 years ago
1
must the mutation spike-in singularity pipeline be processed in a single HPC run?

#105 kiranchari closed 2 years ago
2
AssertionError in makeSomaticScripts.py

#104 Fer020707 closed 2 years ago
8
UnboundLocalError: local variable 'normal_name' referenced before assignment

#103 zhangbiwu closed 2 years ago
14
Recommendations for using your thoroughly vetted High Confidence regions.

#102 SSunkara closed 2 years ago
2
Question: How is the final VAF of variant calculated?

#101 robinjugas closed 2 years ago
2
Error: Training with Strelka leads to Error

#100 robinjugas closed 2 years ago
11
SomaticSeq Prediction Error

#99 robinjugas closed 3 years ago
2
stat /opt/somaticseq/utilities/split_mergedBed.py: no such file or directory error

#98 jeongmeani closed 3 years ago
3
Prediction output files interpretations

#97 wjianga closed 3 years ago
3
Question about SEQ-II datasets

#96 LeiHaoa closed 3 years ago
4
In training mode, error: invalid choice.

#95 wjianga closed 3 years ago
4
Output files when running Consensus mode

#94 wjianga closed 3 years ago
2
omitted some columns of tsv in somatic_vcf2tsv.py

#93 jeongmeani closed 3 years ago
11
bamSimulator result shows a lot of false positives

#92 LeiHaoa closed 3 years ago
4
model overfitting

#91 gianfilippo closed 3 years ago
2
failed prediciton

#90 gianfilippo closed 3 years ago
3
clarification: ada_model_builder_ntChange.R vs ada_model_builder.R

#89 gianfilippo closed 3 years ago
2
Ensemble.sSNV.tsv does not have some vardict variant.

#88 jeongmeani closed 3 years ago
8
multi-thread run clarification

#87 gianfilippo closed 3 years ago
23
submit_callers_multiThreads.sh missing "split" in call to submit_JointSNVMix2.sh

#86 gianfilippo closed 3 years ago
7
singularity submit_SomaticSeq.sh code error ?

#85 gianfilippo closed 3 years ago
2