attrna / ldhat_workflow

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