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.

Optional inputs :

--pmd Input_PMD.txt	Post-mortem damage parameters (see PMD for generating such a file)
--recal recal.txt	Quality score recalibration file (see recal 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

To create a mask of all sites with depth >= indicated value for which at least one non-ref allele was observed. Used when type = nonRef. 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

*_minDepth2_maxDepth1000000_depthMask.bed.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

. $(dirname $0)/find_atlas
. $(dirname $0)/simulate --fixedSeed 50

out="depth"
$atlas --task createMask --type depth --bam simulate.bam --window 4567 \
       --fixedSeed 51 --out $out --logFile $out.out 2> $out.eout

out="nonRef"
$atlas --task createMask --type nonRef --window 7654 \
       --bam simulate.bam --fasta simulate.fasta \
       --fixedSeed 52 --out $out --logFile $out.out 2> $out.eout

out="invariant"
$atlas --task createMask --type invariant --window 5674 --bam simulate.bam \
       --fixedSeed 53 --out $out --logFile $out.out 2> $out.eout

out="variant"
$atlas --task createMask --type variant --window 6745 --bam simulate.bam \
       --fixedSeed 54 --out $out --logFile $out.out 2> $out.eout