5.6 HKY85
Estimating HKY85 genotype Distribution
HKY85 infers the genotype Distribution using the HKY85 substitution model (Hasegawa et al. 1985).
5.6.1 Input
Required inputs :
--bam Input_bam_file.bam |
Input bam file. |
--fasta Input_refrence_genome_file.fasta |
Reference genome. |
Optional inputs :
--pmd "library_type:model_for_5'_read:model_for_3'_read" or --RGInfo |
Library type followed by the model to be used for the 5-prime read-end and the 3-prime read-end which can be either “Exponential” or “Empiric”. All three arguments must be provided as a string, divided by colons (:). e.g. : –pmdModels “doubleStrand:Exponential:Exponential”. Used to specify Post-mortem damage parameters. Can also be provided as a .txt file (see PMDfor generating such a file). Default = Will assume there is no PMD in the data. |
--recal recal_model or --RGInfo |
A common recal model for all read groups. Used to specify Quality score recalibration parameters. Can also be provided as a .txt file (see recal for further information). Default = ‘-’, no recalibration is performed. |
Specific Parameters :
- See Filter parameters to apply specific filters for bases, reads and parsing window setting.
Engine parameters that are common to all tasks can be found here.
5.6.3 Usage Example
#! /bin/bash
# Set atlas path
atlas=$(dirname "$0")/../build/atlas
# Simulate a BAM File with specific HKY85 genotype distribution
$atlas simulate --type "HKY85" --mu 0.71 --thetaG 0.0002 --thetaR 0.003 --logFile simulate.out
# Estimate HKY85 genotype distribution
$atlas HKY85 --bam ATLAS_simulations.bam --fasta ATLAS_simulations.fasta --logFile HKY85.out