DEploid
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DEploid-dev
dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Marko...
``` dEploid \ -vcf "${sample}.vcf.gz" \ -plaf 'Colombia_candidates_PLAF.txt' \ -panel 'Colombia_candidates_reference_panel.txt' \ -o "$sample" \ -best \ -sigma 2.0 zsh: segmentation fault dEploid -vcf "${sample}.vcf.gz" -plaf 'Colombia_candidates_PLAF.txt' -panel ```
**Describe the bug** When run multiple times on the same data set, dEploid oscillates between two different answers. For example, first answer: ``` Effective_K: 1.00005 Inferred_K: 1 Adjusted_effective_K: 1.00005 Proportions:...
- [x] FAQ.md - [ ] Output.md - [x] Pf3k-workflow.md - [x] synopsis.md
Set working examples ....
- seed - sigma - number of samples - burn rate
Take out from DEploidIO // Diagnostics double maxLLKs_; void setmaxLLKs ( const double setTo ) { this->maxLLKs_ = setTo; } double meanThetallks_; void setmeanThetallks ( const double setTo ) {...
sample list for subsets of the big panel, one row for each chrom
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dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Marko...