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
DepthFilter
11.5
Perses
11.6
Pallas
11.7
Troubleshooting
Published with bookdown
9.2
Parameters on Bases
Parameter
Description
Default
--filterBaseQual integer_1,integer_2
Filter out bases with quality outside the range [integer_1,integer_2].
[1,93]
--ignoreContexts
Filter out bases based on context.
keep bases regardless of base context