5.6 summaryStats

Summary statistics per window/genomewide: Felsenstein, HKY85, Pi

summaryStats does summary statistics per window or genometools, and can estimate the genotype Distribution using both the Felsenstein and HKY85 (Hasegawa et al. 1985) substitution models as well as the Pi-distribution.

5.6.1 Input

Required inputs :

--bam file.bam or --glf file.glf.gz	Input bam or glf file.
--fasta reference.fasta	Reference genome.

Optional inputs :

--RGInfo rginfo.json	File defining PMD and quality recalibration parameters. Default is no PMD and no quality recalibration.
--pmd pmd_model	Specify Post-mortem damage parameters.
--recal recal_model	Specify Quality score recalibration parameters.
--prob	--depth
--averageDepth	Average depth of input file, used together with --depth. If none is given, it will be calculated.
--sample reads|sites|upToDepth	Downsample method to use (together with ‘–prob’ or –‘depth’)
--genomeWide	Do summary statistics not on windows, but on whole genome. Needs lot of memory, best use together with --regions
--estimators Felsenstein|HKY85|Pi	Method to be used to calculate heterozygosity. Can be combined. Default = all.

Specific Parameters :

• See Filter parameters to apply specific filters for bases, reads and parsing window setting.

Engine parameters that are common to all tasks can be found here.

5.6.2 Output

5.6.3 Usage Example

# Simulate a BAM File with specific HKY85 genotype distribution
atlas simulate --type "HKY85" --mu 0.71 --thetaG 0.0002 --thetaR 0.003

# Create window-by window summary stats, including estimated HKY85 model
atlas summaryStats --bam ATLAS_simulations.bam --fasta ATLAS_simulations.fasta