NGS-Var2017 Exercise.3
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BWA mapping QC using Picard tools, and Qualimap
Each mapping is unique and can be biased by many unknown factors. Performing QC is essential in each experiment to avoid carryover of errors to the downstream analyses.
Contents
Perform mapping QC using Picard CollectMultipleMetrics
Picard tools include a number of valuable QC programs that can be used separately or with one single command triggering multiple tests as shown next.
- start the Picard.CollectMultipleMetrics module and link the last BAM file from the previous exercise and to the human hg19 reference
- fill additional parameters
- wait and review the PDF and TXT results
Perform integrated BAM QC with the Qualimap GUI
Like what FastQC does for FastQ data, Qualimap can integrate several quality control steps of your BAM data in one go. Qualimap[1] is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI, online help page) for the shy and hurried among you and a command-line interface (online help page) to facilitate the quality control of alignment sequencing data (PDF manual link). We next will show the use of the CLI version for basic BAM QC but as seen in the hidden documentation below, Qualimap proposes many more very attractive tools that are left for you to explore.
A QC on the sample BAM files can be performed in the GUI
The GUI run can be started as shown below
- start Qualimap
- link to files downloaded from the GenePattern server and run
- review the results
Qualimap results saved on the BITS data server
download exercise files
Download exercise files here
References:
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