Atlas Documentation
ATLAS
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
2.3
Typical workflow chart
3
Tutorial
3.1
Data from a Single Individual
3.2
Data from a Population
4
Read tasks
4.1
assessSoftClipping
4.2
BAMDiagnostics
4.3
downsample
4.4
filterBAM
4.5
mergeOverlappingReads
4.6
mergeRG
4.7
PMDS
4.8
qualityTransformation
4.9
readOverlap
4.10
trimSoftClips
5
Site tasks
5.1
allelicDepth
5.2
call
5.3
createMask
5.4
estimateErrors
5.5
GLF
5.6
HKY85
5.7
mutationLoad
5.8
pileup
5.9
PSMC
5.10
theta
5.11
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
polymorphicWindows
6.9
printGLF
6.10
saf
7
VCF Tasks
7.1
convertVCF
7.2
testHardyWeinberg
7.3
VCFCompare
7.4
VCFDiagnostics
8
Simulation Tasks
8.1
simulate
9
File Formats
9.1
Beagle
9.2
geno
9.3
LFMM
9.4
posfile
9.5
genfile
10
Filter parameters
10.1
Filter parameters for Reads
10.2
Filter parameters for bases
10.3
Filter parameters for Parsing window settings
11
Engine parameters
12
ATLAS-Pipeline
12.1
Requirements
12.2
Gaia
12.3
Rhea
12.4
Perses
12.5
Pallas
12.6
Troubleshooting
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Welcome to ATLAS, your guide to the world of low-depth and ancient DNA!
Chapter 9
File Formats