The 2.0 version(BinMarkers-v2) do not require the installation of PDL and GSL.
BinMarkers is a program for creating bin markers from a large set of SNP markers based on their positions on scaffolds/contigs. The purpose of this program is to reduce the number of markers for constructing genetic maps using Joinmap, which limited to about six thousands markers.
- Author: Leiting Li, Chenyong Miao
- Email: [email protected]
- LICENCE: BSD
git clone https://github.com/lileiting/BinMarkers.git
Perl programming language and pmf_binomial function in Perl module PDL::Stats
Dependencies of PDL::Stats
How to install PDL::Stats
perl -MCPAN -e shell
install PDL
install PDL::Stats
or use cpan
cpan PDL
cpan PDL::Stats
or (if without permission to install)
sudo cpan PDL
sudo cpan PDL::Stats
or use cpanp
cpanp -i PDL
cpanp -i PDL::Stats
or use cpanm
cpanm PDL
cpanm PDL::Stats
How to install GSL
Use brew in Mac OS
brew install gsl
Use yum in CentOS
sudo yum install gsl
sudo yum install gsl-devel
Use apt-get in Ubuntu
sudo apt-get install libgsl0ldbl
sudo apt-get install gsl-bin libgsl0-dev
Input data format
Input data should be a matrix, one marker per line, one individual per column. The first line is the title containing individual names, the first column is marker names.
Marker names should contain two parts. First is the scaffold/contig/chromosome name, second is the position, and they were joined by dash or underscore, e.g. scaffold1_12345, scaffold1-12345
The default genotypes are "a" for 0/0, "h" for 0/1, "b" for 1/1, "-" for missingthese could be customized using -0, -1, -2 and -m options.
The default value for threshold is 5, "threshold" means maximum genotype differences allowed within a bin marker block, which similar to maximum allowed mismatch in sequence alignment.
Examples
perl binmarkers.pl markers.map -t 5
perl binmarkers.pl markers.map --threshold 5
perl binmarkers.pl markers.map -t 5 -0 a -1 h -2 b -m '-'
perl binmarkers.pl markers.map --threshold=5 --letter_for_0_0=a --letter_for_0_1=h --letter_for_1_1=b --missing='-'
perl binmarkers.pl markers.map -t 5 -0 a -1 h -2 b -m '-' --error_rate_for_0_0 0.04 --error_rate_for_0_1 0.03 --error_rate_for_1_1 0.01