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Perform target enrichment analysis from a BAM file


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NGSRich [1] is a java tool performing enrichment analysis based on mapping data (Download from:[2]).

First create a small shell script (NGSRich) to start it like follows and place it in the NGSRich /bin folder with executable rights

java -Xmx4G NGSrich $@

You can now run it as it was a cli application. Some info is accessible through the help menu of the Java dry run. There is unfortunately no decent web page to exemplify it.

This is NGSrich, version 0.7.7.
Usage: java NGSrich [command] [options]
	evaluate	Evaluate target enrichment for a single sample.
	summarize	Create a summary report for several evaluations.


NGSRich evaluate
STEP 0: Checking and Validation Step
Checking Requirements: success.
Reading specified parameters: Usage: java NGSrich evaluate -r <readsFile> -u <genome-name> -t <target> 
				[(-a|-g) <annotation>] [-s <sName>] [-T <tmpDir>] 
				[-o <outDir>] [-p <poor> -h <high>] [--no-details>] 
				[--no-sort] [-id <readGroupId>] [-b <baseQuality>] 
				[-m <mapQuality>]
	<readsFile>	Path to read alignment file in SAM or BAM format.
	<genome-name>	UCSC genome version name.
	<target>	Path to target file in BED format.
	<sName>		Sample name [default: prefix of <readsFile>].
	<annotation>	Path of the annotation file [default: download from UCSC].
	<tmpDir>	Temporary directory [default: '/tmp'].
	<outDir>	Output directory [default: '<pathToReadsFile>/enrichment'].
	<poor>		Cutoff for poor coverage [default: 2].
	<high>		Cutoff for high coverage [default: 200].
	<readGroupId>	ID of the read group to be assessed from a multi-sample file.
	<baseQuality>	Minimum phred-scaled quality of a nucleotide to be considered.
	<mapQuality>	Minimum phred-scaled mapping quality of a read to be considered.
	--no-details	Skip computation of the details reports.
	--no-sort	Skip sorting step (if file header is absent).


NGSRich summarize
Usage: NGSrich summarize -i <inputIndex> -o <outDir> [-p <poor> -h <high>]
	<inputIndex>	File with evaluation directories to be summarized, one per line.
	<outDir>	Output directory.
	<poor>		Cutoff for poorly covered genes [default: 2].
	<high>		Cutoff for highly covered genes [default: 200].

  1. Peter Frommolt, Ali T Abdallah, Janine Altmüller, Susanne Motameny, Holger Thiele, Christian Becker, Kathryn Stemshorn, Matthias Fischer, Tobias Freilinger, Peter Nürnberg
    Assessing the enrichment performance in targeted resequencing experiments.
    Hum Mutat: 2012, 33(4);635-41
    [PubMed:22290614] ##WORLDCAT## [DOI] (I p)


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