5.3 createMask

Creating a mask BED file

createMask creates a mask in BED format.

5.3.1 Input

Required inputs :

--bam Input_bam_file.bam	Input bam file.
--type type_of_mask	To indicate the type of mask to be created. Options = depth, nonRef, invariant, variant. See the mask types table for additional information on all available mask types.

Optional inputs :

--recal recal.txt or --RGInfo rginfo.json	Quality score recalibration file (see estimateErrors for further information).
--pmd Input_PMD.txt or --RGInfo rginfo.json	Post-mortem damage parameters (see estimateErrors for further information).
--fasta Input_refrence_genome_file.fasta	Reference genome to calculate percentage of reference bases that are ‘N’ in window. Used when --maxRefN !=1 or type = nonRef

Specific Parameters :

--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.

• 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.

5.3.2 Output

*Mask.bed	To specify a 0-based bed file with regions to be masked. Default = No region is masked.
*_filterSummary.txt	File containing Filter summary of general filter counts.
*_RGInfo.json	File containing read group info.

5.3.3 Usage Example

#! /bin/bash

# Set atlas path
atlas=$(dirname "$0")/../build/atlas

# 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

5.3.4 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.