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
filterBAM
4.5
identifyIlluminaReadGroups - Reassigning read groups based on the platform unit in their name
4.6
liftOver
4.7
mergeOverlappingReads
4.8
mergeRG
4.9
PMDS
4.10
qualityTransformation
5
Site tasks
5.1
allelicDepth
5.2
call
5.3
createMask
5.4
estimateErrors
5.5
GLF
5.6
summaryStats
5.7
mutationLoad
5.8
pileup
5.9
pileupToBed
5.10
PSMC
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
printGLF
6.9
saf
7
VCF Tasks
7.1
convertVCF
7.2
testHardyWeinberg
7.3
VCFCompare
7.4
VCFDiagnostics
8
Other Tasks
8.1
simulate
8.2
sfsStats
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
Getting started
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 8
Other Tasks
simulate
Simulate bam- or vcf-file[s]
sfsStats
Estimate expected heterozygosity and Fst from 2D SFS