LDhelmet¶
LDhelmet is a tool to Fine-scale recombination rate estimation from population genetic data.
LDhelmet is available as a module on Apocrita.
Usage¶
To run the latest installed version of LDhelmet, simply load the ldhelmet
module:
module load ldhelmet ldhelmet -h Usage: ldhelmet <command> [args]
For usage documentation, run ldhelmet -h
.
Example job¶
Serial job¶
Here is an example job running on 2 cores and 4GB total memory:
#!/bin/bash #$ -cwd #$ -j y #$ -pe smp 2 #$ -l h_rt=2:0:0 #$ -l h_vmem=2G module load ldhelmet ldhelmet find_confs --num_threads ${NSLOTS} \ -w 50 \ -o output.conf \ input.fasta ldhelmet table_gen --num_threads ${NSLOTS} \ -t 0.008 \ -r 0.0 0.1 10.0 1.0 100.0 \ -c output.conf \ -o output.lk ldhelmet pade --num_threads ${NSLOTS} \ -t 0.008 \ -x 12 \ --defect_threshold 40 \ -c output.conf \ -o output.pade ldhelmet rjmcmc --num_threads ${NSLOTS} \ -l output.lk \ -p output.pade \ -m mut_mat.txt \ -s input.fasta \ -b 50 \ --burn_in 10000 \ -n 100000 \ -o output.post ldhelmet post_to_text -m \ -p 0.025 \ -p 0.50 \ -p 0.975 \ -o output.txt \ output.post ldhelmet max_lk --num_threads ${NSLOTS} \ -l output.lk \ -p output.pade \ -m mut_mat.txt \ -s input.fasta