Quick and dirty pipeline for running LDhat.
Purpose
Simple pipeline to run LDhat and estimate variable recombination rates
To obtain realistic results, the pipeline splits whole genome data into small chunk of 2,000 - 5,000 SNPs before running the different programs from LDhat
Dependencies
LDhat available here
vcftools software available here
python3.6
GNU parallel (installed by default on most linux cluster)
software installation
#ldhat:
make
#then add path to bashrc or cp to bin
#vcftools
git clone https://github.com/vcftools/vcftools.git
./autogen.sh
./configure --prefix=/path/to/vcftools/
make
make install
#then add path to bashrc or cp to bin
Running the pipeline
input needed: vcf file split by populations.
vcf file should be stored in 00-data and named as follows:
batch."$pop".recode.vcf where "$pop" is the name of the target population
to create input files:
./02-script/00-extract_data.sh population_name list_chromosome
Running interval and rhomap
first make sure you have an appropriate lk file.
Such file can be obtained from lkgen or from running complete.
Setting LDhat parameters
Edit files 02.interval_iteration.sh and 03.rhomap_iteration.sh
in 02-scripts
to choose appropriate MCMC length, and other relevand parameters.
Then edit files
02-scripts/graham_cedar/04.interval_parallel_NC_arg.sh and
02-scripts/graham_cedar/05.rhomap_parallel_NC_arg.sh
to match your cluster requirement end run the script
Please read the manual and LDhat papers before use
References
A. Auton and G. McVean. Recombination rate estimation in the presence of hotspots. Genome Res., 2007