Overview

Randomly sample one base per site. We generally recommend using the allelePresence caller instead of the randomBaseCaller.

Input

• BAM file

Output

• a gzipped file containing the calls in .txt format with chr, pos, sequencing depth, pileup of bases covering the site, random base

Usage Example

The required syntax to launch ATLAS as the randomBaseCaller is:

./atlas task=randomBaseCaller bam=example.bam verbose

Engine Parameters

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