luntergroup / octopus

Bayesian haplotype-based mutation calling

luntergroup/octopus Issues

Starting Call Set Refinement (CSR) filtering provokes RAM overload
Updated 3 days ago
Forest file is still not available for donwloading "std::bad_alloc Error"
Updated 15 days ago9
Encountered an exception during calling 'std::bad_alloc'
Updated 16 days ago2
ERROR in reading reference index.
Updated a month ago2
Build fails, is there a singularity?
Updated 2 months ago1
Build failures on `gcc-13`: `option_collation.cpp:1298: error: redundant move in initialization`
Updated 3 months ago
training data & regions of the genome used for somatic random forest model
Updated 4 months ago
Models for NovaseqX?
Updated 6 months ago
Position of maternal or paternal haplotypes in Octopus after performing TRIO analyses
Updated 6 months ago1
Can octopus add a feature to add supported read query names of the variants in the INFO field of the output VCF file?
Updated 6 months ago1
Will octopus add a mode using paired information to compose a linked debruijn graph?
Updated 6 months ago
Population-level variant calling using accessions with complex ploidy level
Updated 7 months ago
info on UL nanpore reads
Updated 8 months ago2
VCF file is empty
Updated 8 months ago
Failed to download forest somatic.v0.7.4.forest.gz
Closed 9 months ago8
Call in high heterozygotes
Closed 8 months ago
elongated runtimes for deep-sequencing data in cancer calling mode
Updated 9 months ago3
Remove depreciated inheritance of std::unary_function
Updated 9 months ago
can not download the forest files
Closed 9 months ago1
Polyclone caller produces VCF records with variable numbers of genotypes across records
Closed 10 months ago2
failed in compilation
Updated 10 months ago
germline.v0.7.4.forest.gz
Closed 10 months ago6
Please let the user decide, if the files are okay ....
Updated 10 months ago1
This is not a bug. Tell us about the issues with the forest files
Closed 10 months ago1
How to install forest model with conda installed version?
Updated a year ago1
GCA_000001405.15_GRCh38_no_alt_analysis_set.fna is not a valid fasta file.
Updated a year ago1
--refcall POSITIONAL reports * instead of . in ALT column for reference call creating triallelic calls downstream
Updated a year ago
Empty VCF file
Updated a year ago
Floating point exception and seg fault in Call Set Refinement with polyclone
Updated a year ago
Possible typo in the documentation
Updated a year ago
Absolute input file paths are appended to working directory paths
Closed a year ago1
Question: Is possible to run Octupus with RNA-seq data?
Updated a year ago2
Question: Calling non-variant sites
Closed 2 years ago11
reference calls for re-genotyping individual sample given (-c) sites
Updated 2 years ago1
Error building on macOS 12.5.1
Closed 2 years ago
Job killed due to `ContigRegion: expanding past contig start`
Updated 2 years ago
Provide optimal parameters for candidate generation
Updated 2 years ago
Can't see realigned bams in the latest IGV on windows
Closed 2 years ago1
"PASS" variants Octopus detects also have tons of alternate reads in the normal sample
Updated 2 years ago
AVX support
Updated 2 years ago
Segmentation fault when running Cell command
Updated 2 years ago
Install fails on Apple M1
Updated 2 years ago1
Segmentation fault when reference genome contains '.'
Updated 2 years ago1
very slow call set refinement with refcall
Updated 2 years ago1
very low -B, safe? && core dump 'what(): BadRegionCompare:'
Updated 2 years ago1
ERROE:Phred: negative error probability -0.000000
Updated 2 years ago6
When would an insertion's base be called as N?
Closed 2 years ago2
Error with same phase set, but different genotype ploides
Closed 2 years ago1
somatic calling: inconsistent ploidy
Updated 2 years ago5
INFO/MQ Float in VCF v4.3
Closed 2 years ago1