A small pipeline designed to call variants on haploids genome. Configuration file is for the cc2 cluster in cirad.
- python 3 and 2
- script fastqCombinedPairedEnd.py (provided in the repo): used to synchronize read pairs if you cleaned them independantly.
- snakemake
- bwa
- freebayes
- vcffilter (comes with freebayes)
- samtools
- picard tools
file VARHAP.snake needs to be edited in order to:
- specify data directory (several reads pair can be analyzed jointly
- Reference sequences on which mapping should be done (fasta format)
- extension of file name (reads R1) should be specified
- module load should work as such Then you can try:
module load system/python/3.4.3
snakemake -s VARHAP.snake --jobs 12 --cluster "qsub -q normal.q -cwd -V -pe parallel_smp {threads}" -r