5.9 pileupToBed

Create bed file from pileup file

pileupToBed creates a bed-file using the output of pileup and a depth filter. This is especially useful when running pileup over several bamfiles.

5.9.1 Input

Required inputs :

--pileup pileup.txt.gz	Pileup output file
--depth integer_value1,integer_value2	To filter out sites with sequencing depth outside the range [integer_value1,integer_value2]

5.9.2 Output

*_pileup.bed

0-based BED-file with regions within the depth-mask.

5.9.3 Usage Example

#! /bin/bash

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

# Simulate 5 BAM Files in Hardy–Weinberg Equilibrium
$atlas simulate --type HW --sampleSize 5 --logFile simulate.out

# Create pileup file of all bam files and name it multiBam
$atlas pileup --bam "$(ls *.bam)" --logFile pileup.out --out multiBam

# Create bed file from pileup output with 5 <= depth < 30
$atlas pileupToBed --pileup multiBam_pileup.txt.gz --depth "[10,30)" --logFile pileupToBed.out