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
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Chapter 10
File Formats
Beagle
geno
LFMM
posfile
genfile