luntergroup octopus issues

luntergroup / octopus

Bayesian haplotype-based mutation calling

MIT License

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issues

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Use with Nanopore long reads

#281 pabloangulo7 opened 4 weeks ago
1
Starting Call Set Refinement (CSR) filtering provokes RAM overload

#280 amolares opened 1 month ago
2
ERROR in reading reference index.

#279 Knnnk opened 2 months ago
2
Build fails, is there a singularity?

#278 ESDeutekom opened 4 months ago
1
Build failures on `gcc-13`: `option_collation.cpp:1298: error: redundant move in initialization`

#276 trofi opened 4 months ago
0
training data & regions of the genome used for somatic random forest model

#275 omicsnut opened 5 months ago
0
Encountered an exception during calling 'std::bad_alloc'

#274 Ankita-1211 opened 7 months ago
2
Models for NovaseqX?

#273 cnk113 opened 7 months ago
0
Position of maternal or paternal haplotypes in Octopus after performing TRIO analyses

#272 bosamu05 opened 8 months ago
1
Can octopus add a feature to add supported read query names of the variants in the INFO field of the output VCF file?

#271 yangyxt opened 8 months ago
1
Will octopus add a mode using paired information to compose a linked debruijn graph?

#270 yangyxt opened 8 months ago
0
Population-level variant calling using accessions with complex ploidy level

#269 mirror110 opened 8 months ago
0
Forest file is still not available for donwloading "std::bad_alloc Error"

#268 hfl112 opened 8 months ago
9
info on UL nanpore reads

#267 gambalab opened 9 months ago
2
VCF file is empty

#266 Axze-rgb opened 9 months ago
0
Call in high heterozygotes

#265 Axze-rgb closed 9 months ago
0
Remove depreciated inheritance of std::unary_function

#264 GWW opened 10 months ago
0
can not download the forest files

#263 lfalive closed 10 months ago
1
This is not a bug. Tell us about the issues with the forest files

#262 Axze-rgb closed 11 months ago
1
germline.v0.7.4.forest.gz

#261 gambalab closed 11 months ago
6
Please let the user decide, if the files are okay ....

#260 HMPNK opened 1 year ago
1
Failed to download forest somatic.v0.7.4.forest.gz

#259 Axze-rgb closed 10 months ago
8
Polyclone caller produces VCF records with variable numbers of genotypes across records

#258 gtollefson closed 11 months ago
2
--refcall POSITIONAL reports * instead of . in ALT column for reference call creating triallelic calls downstream

#257 Kelzor opened 1 year ago
0
GCA_000001405.15_GRCh38_no_alt_analysis_set.fna is not a valid fasta file.

#256 gitterspec opened 1 year ago
1
Empty VCF file

#255 543090lee opened 1 year ago
0
Floating point exception and seg fault in Call Set Refinement with polyclone

#254 slhogle opened 1 year ago
0
Possible typo in the documentation

#253 gtollefson opened 1 year ago
0
failed in compilation

#252 lmanchon opened 1 year ago
0
Question: Is possible to run Octupus with RNA-seq data?

#251 alejandrogzi opened 1 year ago
2
Absolute input file paths are appended to working directory paths

#250 TBradley27 closed 1 year ago
1
Question: Calling non-variant sites

#249 ja-Reeve closed 1 year ago
11
Provide optimal parameters for candidate generation

#248 jdidion opened 1 year ago
0
Error building on macOS 12.5.1

#247 nuin closed 1 year ago
0
Can't see realigned bams in the latest IGV on windows

#246 waalkes closed 1 year ago
1
reference calls for re-genotyping individual sample given (-c) sites

#245 brentp opened 1 year ago
1
Job killed due to `ContigRegion: expanding past contig start`

#244 ja-Reeve opened 1 year ago
0
"PASS" variants Octopus detects also have tons of alternate reads in the normal sample

#243 Mathieu179 opened 1 year ago
0
Segmentation fault when running Cell command

#242 chenv3 opened 1 year ago
0
AVX support

#241 skchronicles opened 1 year ago
0
How to install forest model with conda installed version?

#240 yangyxt opened 1 year ago
1
very slow call set refinement with refcall

#239 nemartins opened 1 year ago
1
Segmentation fault when reference genome contains '.'

#238 bricoletc opened 2 years ago
1
very low -B, safe? && core dump 'what(): BadRegionCompare:'

#237 iamh2o opened 2 years ago
1
Install fails on Apple M1

#236 jdidion opened 2 years ago
1
ERROE:Phred: negative error probability -0.000000

#235 xixi1998815 opened 2 years ago
6
When would an insertion's base be called as N?

#234 js72587 closed 2 years ago
2
Error with same phase set, but different genotype ploides

#233 cnk113 closed 2 years ago
1
elongated runtimes for deep-sequencing data in cancer calling mode

#232 iserf opened 2 years ago
3
INFO/MQ Float in VCF v4.3

#231 jdm204 closed 2 years ago
1