qBasePileup

• Introduction
• Installation
• Usage
• Modes

Introduction

qbasepileup performs pileup on positions of interest and produces base coverage information and various others metrics on the reads at those position.

Installation

qbasepileup requires java 7 and (ideally) a multi-core machine (5 threads are run concurrently) with at least 20GB of RAM.
Download the qbasepileup tar file
Untar the tar file into a directory of your choice
You should see jar files for qbasepileup and its dependencies:

[oholmes@minion0 qbasepileup]$ tar xjvf qbasepileup.tar.bz2
x antlr-3.2.jar
x ini4j-0.5.2-SNAPSHOT.jar
x jopt-simple-3.2.jar
x picard-1.110.jar
x qbamfilter-1.0pre.jar
x qcommon-0.1pre.jar
x qio-0.1pre.jar
x qpicard-0.1pre.jar
x qpileup-0.1pre.jar
x sam-1.110.jar
x jhdfobj.jar
x jhdf5obj.jar
x jhdf5.jar
x jhdf.jar
[oholmes@minion0 qbasepileup]$

Usage

java -jar qbasepileup.jar [OPTIONS] -m mode -i file.bam -r ref.fa -s positions.txt -o pileup.txt -log file.log

Modes

Mode	Description
SNP	reads one or more BAM files, a reference genome, and a file containing positions of SNPs. It finds the reference genome base at the SNP position as well as the bases found at that position in all reads aligned to that region. Coverage per nucleotide is reported and the total coverage at that position is reported. By default, duplicates and unmapped reads are excluded.
Compound SNP	reads one or more BAM files, a reference genome, and a file containing positions of compound SNPs (SNPs that sit next to each other). It finds the reference genome base at the compound SNP positions as well as the bases found at that position in all reads aligned to that region. Coverage per nucleotide is reported and the total coverage at that position is reported. By default, the filter is: and(Flag_DuplicateRead==false , CIGAR_M>34 , MD_mismatch <= 3 , option_SM > 10)
Indel	reads tumour and normal BAM files, a reference genome, and somatic and/or germline files containing positions of indels and pileups the reads around the indel to count a number of metrics. Metrics include: total reads, number of reads that span the indel, number of reads with the indel, number of novel starts with the indel, number of reads with nearby soft clipping and number of reads with nearby indels.
Coverage	reads one or more BAM files, and a file containing reference ranges and piles up the reads around the indel to count the number of reads covering each position in the range.