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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 default 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

Reference