bamaddrg

Adds read groups to input BAM files, streams BAM output on stdout.

This is intended for use "fixing up" RG tags on the fly so that they reflect the source file from which the aligment originated from. This allows the "safe" merging of many files from many individuals into one stream, suitable for input into downstream processing systems such as freebayes (a population variant detector).

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Requirements

g++

BAMtools

> lib/libbamtools.a

> include/bamtools/api/BamMultiReader.h

> include/bamtools/api/BamWriter.h

> include/bamtools/api/SamReadGroup.h

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Install

Install BAMtools

cd $BamtoolsInstallDir

git clone git://github.com/pezmaster31/bamtools.git

cd bamtools

mkdir build

cd build

cmake -DCMAKE_INSTALL_PREFIX=$PWD/../../x86_64 ..

export BAMTOOLS_ROOT=$PWD/../../x86_64

make

make install

Install bamaddrg

cd $BamaddrgInstallDir

git clone https://github.com/lufuhao/bamaddrg.git

mv bamaddrg x86_64

cd x86_64

make

#or

make =/path/to/bamtools/root

If make report error, replace following $BamtoolsInstallDir. and try again

g++ -O3 -I$BAMTOOLS_ROOT/include/bamtools -L$BAMTOOLS_ROOT/lib  bamaddrg.cpp -o bamaddrg -lbamtools -lz

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Usage:

To tag multiple files simultaneously, use as such:

% bamaddrg -b file1.bam -s jill -r group.s1.1 \
           -b file2.bam -s jill -r group.s1.2 \
           -b file3.bam -s bill \
           -b file4.bam \
   | freebayes ...

This would add the sample name "jill" to records from file1.bam and file2.bam, while specifying that specific read group identify alignments from each file. Alignments from file3.bam would be tagged with sample name "bill" and read group id "bill", and samples from file4.bam would be tagged with sample name "file4.bam" and read group id "file4.bam."