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

bcftools software availablehere

vcftools software available here

python3

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 splitted by populations. An example script to split by pop is available in utility_scripts

to create input files: ./02-script/00-extract_data_bcftools.sh population_name list_chromosome

Running interval and rhomap

first make sure you have an appropriate lk file (see manual)

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 relevants 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 and run the script

Generating a lookup table

• please see very simple example scripts located in 02-scripts/complete/

Please read the manual and LDhat papers before use

#To do:

• add angsd for estimating theta

References

A. Auton and G. McVean. Recombination rate estimation in the presence of hotspots. Genome Res., 2007