Overview

BAMDiagnostics calculates the mean sequencing depth across the whole genome, the mapping quality distribution, the read length distribution and the fragment length distribution (only known for paired-end data). The mean sequencing depth is calculated by dividing the total length of all aligned bases by the length of the genome in the BAM file.

Input

• A BAM file

Output

• Depth estimate with suffix _approximateDepth.txt
• Mapping quality distribution with suffix _MQ.txt
• Read length distribution with suffix _readLength.txt
• Fragment length mean and variance for paired-end reads with suffix _fragmentStats.txt. This file will be empty if there are no proper pairs in the BAM file

The statistics are listed in respective file first for the total BAM file and then separately for the different read groups.

Usage Example

./atlas task=BAMDiagnostics bam=example.bam readGroup=first_readGroup_name verbose #limit analysis to first read group

Specific Arguments

• maxMQ: set the maximum mapping quality ATLAS should expect. If too small, ATLAS will throw an error. Default = 100.
• maxReadLength: set the maximum read length ATLAS should expect. If too small, ATLAS will throw an error. Default = 1000.

Engine Parameters

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