Overview

This task creates a depth mask in BED format

Input

• A BAM file

Output

• A 0-based bed file with regions to be masked

Usage Example

./atlas task=createDepthMask minDepthForMask=0 maxDepthForMask=10000000

Parameters

• minDepthForMask: Sites with depth < minDepthForMask will be written to the BED file
• maxDepthForMask: Sites with depth > maxDepthForMask will be written to the BED file

Engine Parameters

Engine parameters that are common to all tasks can be found here.