This software is a simple query language for filtering SAM/BAM sequences.
Ubuntu users can install from the PPA by executing:
sudo apt-add-repository ppa:boutroslab/ppa && sudo apt-get update && sudo apt-get install bamql
In order to compile, LLVM 3.4 - 4.0, HTSlib, and libuuid are required. If compiling using GCC, version 4.9 or later is required.
On Debian/Ubuntu, these can be installed by:
sudo apt-get install autotools-dev build-essential libhts-dev libtool libpcre++-dev llvm-dev pkg-config uuid-dev zlib1g-dev
On RedHat/Fedora, these can be installed by:
sudo yum groupinstall "Development Tools"
sudo yum install libtool pcre-devel llvm-devel pkgconfig libuuid-devel zlib-devel
and HTSlib must be installed from sources.
In the source directory,
autoreconf -i && ./configure && make && sudo make install
The language consists of a number of predicates, things which match sequences, and connectives, which compose predicates.
For example, the following query will match sequences on chromosome 7 which are from the read group labelled “RUN3”:
chr(7) & read_group : RUN3
To filter read, use bamql like this:
bamql -i input.bam -o reads_i_live.bam -O reads_i_loathe.bam 'chr(7) & read_group : RUN3'
The following will take a sub-sample for mitochondrial sequences and all the sequences that have matched to chromosomes starting with “ug”:
chr(M) & random(0.2) | chr(ug*)
Again, to filter, use bamql like this:
bamql -f input.bam -o mitochondrial_subsample_with_traps.bam 'chr(M) & random(0.2) | chr(ug*)'
The details can be found in the manual page, which can be viewed by typing man bamql_queries at the command prompt or view the manual online.