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
GLF
5.7
mutationLoad
5.8
pileup
5.9
pileupToBed
5.10
PSMC
5.11
summaryStats
5.12
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
9.2
Parameters on Bases
9.3
Parameters on Reads
9.4
Parameters on Sites
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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Welcome to ATLAS, your guide to the world of low-depth and ancient DNA!
5.2
bed
Join bed files: region + mask, union or intersect