Comments (2)
dancooke
commented on August 30, 2024
The "N + 1" problem is discussed in the wiki pages here. Calling of large cohorts has not been tested, and joint calling of sex chromosomes is currently under development (see this issue).
The current develop branch version supports reference calling (see this wiki page). Note however that Octopus does not report genotype likelihoods, so you will not be able to use GATK-style gVCF merging.
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simoncawley
commented on August 30, 2024
Hi Dan, I'm interested in trying out Octopus for calling reference, I was excited to see the link you posted above but sadly it leads to a blank page. Is there any documentation available in another location?
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Related Issues (20)
- can not download the forest files HOT 1
- Remove depreciated inheritance of std::unary_function
- Call in high heterozygotes
- VCF file is empty
- info on UL nanpore reads HOT 2
- Forest file is still not available for donwloading "std::bad_alloc Error" HOT 9
- Population-level variant calling using accessions with complex ploidy level
- Will octopus add a mode using paired information to compose a linked debruijn graph?
- Can octopus add a feature to add supported read query names of the variants in the INFO field of the output VCF file? HOT 1
- Position of maternal or paternal haplotypes in Octopus after performing TRIO analyses HOT 1
- Models for NovaseqX?
- Encountered an exception during calling 'std::bad_alloc' HOT 2
- training data & regions of the genome used for somatic random forest model
- Build failures on `gcc-13`: `option_collation.cpp:1298: error: redundant move in initialization`
- Build fails, is there a singularity? HOT 1
- ERROR in reading reference index. HOT 2
- Starting Call Set Refinement (CSR) filtering provokes RAM overload HOT 2
- Use with Nanopore long reads HOT 2
- After recompiling from source get error 'Phred: negative error [2024-07-15 12:55:12] <EROR> probability -0.000000' HOT 2
- Binaries compiled for AVX-512 cores do not process the whole genome. HOT 2
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