This workflow is developped in Louis Bernatchez' lab.
WARNING
The software is provided "as is", without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose and noninfringement. In no event shall the authors or copyright holders be liable for any claim, damages or other liability, whether in an action of contract, tort or otherwise, arising from, out of or in connection with the software or the use or other dealings in the software.
git clone https://github.com/samtools/htslib.git
git clone https://github.com/ANGSD/angsd.git
cd htslib;make;cd ../angsd ;make HTSSRC=../htslib
sbatch 00_scripts/01_cutadapt.sh
sbatch 00_scripts/02_demultiplexing.sh
sbatch 00_scripts/03_mapping_gsnap.sh
ls -1 03_mapped/*.bam > 01_info_files/list_bam
sbatch 00_scripts/04_genotyping.sh
In progress
Korneliussen T. S., Albrechtsen A. and Nielsen R. 2014. ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinformatics. DOI: 10.1186/s12859-014-0356-4
This workflow is licensed under the GPL3 license. See the LICENCE file for more details.