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Clone wikiATLAS / Population Genetic Tools: inbreeding coefficient F
Overview
VCF files with GL and PL work. Run several burnins to optimize the widths of the proposal functions.
Input
- VCF file, created by e.g. ATLAS task major/minor
- txt file (optional): e.g. samplesPopulations.txt
This file is a user-created .txt file containing the samples to be used and their population affiliation. Different allele counts will be estimated for different populations
Example:
sample1 1 sample2 1 sample5 2 sample8 2 |
|
Output
- A text file with suffix _inbreedingMCMC.txt: This file contains the samples from the posterior distribution of the parameters F, gamma, pi, and a given number of allele frequencies.
- A text file with suffix _inbreedingMCMC_posteriors.txt.gz: This file contains information about the posteriors of the parameter values. One of these files is written to disk every 1000 iterations.
Usage Example
./atlas task=inbreeding vcf=example.vcf.gz
Specific Arguments
Reading vcf:
- samples: specify samples to be used and their population affiliation
- limitLines: amount of lines to be read from VCF file
- minDepth: only store sites with minimum depth
- minSamplesWithData: only store sites with minimum number of samples. Default = 1
- minMAF: only store sites where initial estimate of allele frequency is larger or equal to minMAF. Default = 0.0
- minVariantQuality: only store sites with minimum variant quality
- reportFreq: after how many lines the reading progress is printed to the terminal. Default = 10000.
- epsF: epsilon for EM algorithm to estimate allele frequencies. Default = 0.0001
MCMC:
- writeBurninToFile: write values samples during burnins to the results file.
- trueAlleleFreq: provide file with true allele frequencies (for debugging)
- thinning: only print every \(n^{th}\) iteration to the results file. Default = 1 (all)
- numBurnins: number of burn-in rounds should that should be run. Default = 1
- burninLength: number of iterations in each burn-in round. Default = 1000
- numIter: number of iterations in the MCMC run
- probMovingToModelNoF: probability of proposing move to model \(M_0\)
Updated