5.4 createMask

Creating a mask BED file

createMask creates a mask in BED format.

5.4.1 Mask types

depth Creates a mask for all sites whose depth falls outside the specified range.
nonRef Creates a mask for all sites with depth above the minimum threshold where at least one non‑reference allele is observed.
invariant Creates a mask for all sites with depth above the minimum threshold where only a single allele is observed.
variant Creates a mask for all sites with depth above the minimum threshold where multiple alleles are observed.

5.4.2 Parameters

5.4.2.1 Input

--bam Input_bam_file.bam Input bam file.
--type type_of_mask Indicate the type of mask to be created. Options = depth,nonRef,invariant,variant (see the mask types table)

5.4.2.2 Specific

--minDepthForMask integer_value Minimum sequencing depth that a site needs to have to be added to the mask, in addition to other requirements specified by --type. Default = 2.

5.4.3 Output

*Mask.bed Specify a 0-based bed file with regions to be masked. Default = No region is masked.

5.4.4 Usage Example

# Simulate a BAM File
atlas simulate

# Create mask for depth within [5, 10]
atlas createMask --type depth --minDepth 5 --maxDepth 10 --bam ATLAS_simulations.bam