• Atlas Documentation
  • ATLAS and the ATLAS-pipeline
  • 1 Getting started
    • 1.1 Installation using Conda
    • 1.2 Installation from source
    • 1.3 Running ATLAS
    • 1.4 Quickstart
  • 2 Workflows
    • 2.1 Low-depth sequencing
    • 2.2 Ancient DNA
  • 3 Tutorial
    • 3.1 Data from a Single Individual
    • 3.2 Data from One Population
    • 3.3 Data from many Populations
  • 4 Read tasks
    • 4.1 assessSoftClipping
    • 4.2 BAMDiagnostics
    • 4.3 downsample
    • 4.4 extractReads
    • 4.5 filterBAM
    • 4.6 identifyIlluminaReadGroups
    • 4.7 liftOver
    • 4.8 mergeOverlappingReads
    • 4.9 mergeRG
    • 4.10 PMDS
    • 4.11 qualityTransformation
  • 5 Site tasks
    • 5.1 allelicDepth
    • 5.2 bed
    • 5.3 call
    • 5.4 createMask
    • 5.5 estimateErrors
    • 5.6 DStat
    • 5.7 GLF
    • 5.8 mutationLoad
    • 5.9 pileup
    • 5.10 pileupToBed
    • 5.11 PSMC
    • 5.12 summaryStats
    • 5.13 thetaRatio
  • 6 Population tasks
    • 6.1 alleleCounts
    • 6.2 alleleFreq
    • 6.3 ancestralAlleles
    • 6.4 calculateF2
    • 6.5 geneticDist
    • 6.6 inbreeding
    • 6.7 majorMinor
    • 6.8 printGLF
    • 6.9 saf
  • 7 VCF Tasks
    • 7.1 convertVCF
    • 7.2 testHardyWeinberg
    • 7.3 VCFCompare
    • 7.4 VCFDiagnostics
  • 8 Other Tasks
    • 8.1 sfsStats
    • 8.2 simulate
  • 9 Engine parameters
    • 9.1 General Parameters
    • 9.2 Parameters on Bases
    • 9.3 Parameters on Reads
    • 9.4 Parameters on Sites
    • 9.5 Population Parameters
    • 9.6 Genome Parameters
  • 10 File Formats
    • 10.1 Beagle
    • 10.2 geno
    • 10.3 LFMM
    • 10.4 posfile
    • 10.5 genfile
  • 11 ATLAS-Pipeline
    • 11.1 Getting started
    • 11.2 Gaia
    • 11.3 Rhea
    • 11.4 Perses
    • 11.5 Pallas
    • 11.6 Troubleshooting
  • Published with bookdown

Chapter 9 Engine parameters

  • General parameters
  • Base parameters
  • Read parameters
  • Site parameters
  • Population parameters
  • Genome parameters