5.12 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.

5.12.1 Parameters

5.12.1.1 Input

--bam bamFile.bam Input bam file
--glf glfFile.glf.gz Input glf file
--fasta reference.fasta Reference genome
  • You need to specify either --bam or --glf

5.12.1.2 Specific

--estimators est1,est2,est3 List of estimators to calculate heterozygosity: Felsenstein, HKY85 and Pi. Default = all
--genomeWide Do summary statistics on whole genome, not on windows. Needs lot of memory, best use together with --regions (see genome parameters)
--prob Perform downsampling experiment using given probabilities
--depth Perform downsampling experiment using depths
--averageDepth Average depth of input file, used together with --depth. Will be calculated if not given.
--sample method Downsample method to use: reads, sites or upToDepth. Default= reads

5.12.2 Output

5.12.3 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