5.1 allelicDepth

Adding sites to allelic depth table

allelicDepth creates a table summarizing the composition of the bases covering each site. It is basically a flattened 4-dimensional table.

5.1.1 Parameters

5.1.1.1 Input

--bam Input_bam_file.bam Input BAM file

5.1.1.2 Specific

Parameter Description Default
--printAll Print cells with zero counts as well. Only print cells with non-zero counts

5.1.2 Output

*_allelicDepth.txt.gz A table with the following columns: 1) A,C,G,T: 4 columns listing the amount of bases of each type. 2) Counts: the number of sites that have this specific base composition. 3) Depth: the total depth of the base composition (equal to sum of columns A,C,G and T).

5.1.3 Usage Example

# Simulate a BAM File
atlas simulate

# Create allelicDepth histogram, limit depth to 100
atlas allelicDepth --readUpToDepth 100 --bam ATLAS_simulations.bam