This software is a simple query language for filtering SAM/BAM sequences.

In order to compile, LLVM 14, HTSlib, and libuuid are 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.