UGAT
implements a method to fit an exponential decay to the first 20 base
pairs of C-to-T conversions typically observed in ancient DNA (aDNA) sequencing
data.
A BAM file is needed with reads aligned to a suitable reference genome. From
these alignments, substitution patterns are extracted with the help of htslib
,
and the frequency of C-to-T conversions at the first 20 bases from the 5โ-end is
extracted.
This frequency pattern is then used to fit an exponential decay with a non-linear least squares regression using the Levenberg-Marquardt algorithm implemented in the GNU Scientific Library. From the best fit parameters, a one-sided p-value of the rate parameter is reported to test for significant exponential decay.
To test how this p-value behaves for specified numbers of sequences, UGAT
also
implements two ways of subsampling alignments from the BAM file either by
specifying a target number or target fraction of alignments to sample.
For more background see also the publication at elife, which describes an
R
-based version of the method re-implemented here.
UGAT
makes use of two external libraries, which are included as submodules in
this repository. These libraries are the GNU Scientific Library (GSL
), and
htslib
.
To get the UGAT
source code, as well as the required library code, clone the
repository recursively:
git clone --recursive https://github.com/clwgg/ugat
Please note, that you will need libtool
installed to compile the GSL
library, along with the regular GNU toolchain for compilation.
After cloning, first compile the submodules, and then the UGAT
code:
cd ugat
make submodules
make
This will create the static ugat
binary, which you can copy or move
anywhere for subsequent use.
When updating to the current version, please make sure to also update the submodules:
git pull origin master
git submodule update
make submodules
make
Usage: ./ugat [options] Options: -b - BAM file -n - Number to subsample (in conflict with -f) -s - Seed for random subsample -f - Fraction to subsample (in conflict with -n) -t - Show C to T fraction at first 20 bases instead of exp-fit p-value -c - Just count alignments in BAM file, no subsampling is done (conflict with -f, -n, -t and -s)