5.6 DStat

ABBA-BABA statistic

DStat creates ABBA-BABA statistics, either by random sampling or by accumulationg ABBA/BABBA probabilities over all sites.

5.6.1 Parameters

5.6.1.1 Input

--bam 1.bam,2.bam,3.bam,4.bam

Bam-files of the 4 samples to compare

5.6.1.2 Specific

Parameter	Description	Default
–sample	sample a random base per site and bam-file	accumulate probabilities
–filterTransitions	filter out AG and CT ABBA combinations	use all combinations
–alleles	only use ref and alt base for pattern (see Genome Parameters)	no alleles used

5.6.1.3 Engine

• General
• Bases
• Reads
• Sites
• Genome

5.6.2 Output

*.txt.gz

Table with all counts and DStat

5.6.3 Usage Example

# Simulate a BAM File
atlas simulate --sampleSize 4 --out sim

atlas --task DStat --bam sim_ind1.bam,sim_ind2.bam,sim_ind3.bam,sim_ind4.bam