SNAPE-pooled

Introduction

SNAPE-pooled computes the probability distribution for the frequency of the minor allele in a certain population, at a certain position in the genome. Obviously if this probability is high enough, then you have a segregating position, a.k.a. SNP.

Futher information

If you want to use SNAPE-pooled, I guess you should first read the paper SNP calling by sequencing pooled samples (Raineri E, Ferretti L, Esteve-Codina A, Nevado B, Heath S, Pérez-Enciso M. , BMC Bioinformatics. 2012 Sep 20;13:239. doi: 10.1186/1471-2105-13-239) which explains the formulae used in it.

There is a Postscript manual in the Downloads section of this site. We are distributing the source code, but not an executable : hence you'll have to create a binary yourself, by using the enclosed Makefile. If you don't know how to do that, send me an email.

SNAPE is not a difficult software to run. The input format is SAMTOOLS' pileup and a typical incantation goes as follows: ./snape-pooled -nchr 10 -theta 0.001 -D 0.1 -fold folded \ -priortype informative < example.pileup

Source code

You can browse the source code from this website, namely here and you can download it using SVN ,e.g. by doing:

svn checkout http://snape-pooled.googlecode.com/svn/trunk/ snape-pooled-read-only

The code is distributed under the GNU GPLv3 License.

If you have doubts on how exactly to download or use the package, feel free to contact me or the other project administrators.

Emanuele