About

This is a Nextflow pipeline built around the RFMix2 software for the local genetic ancestry estimation using phased data and reference panel.

Prerequisites

1. Download and install the RFMix2 from https://github.com/slowkoni/rfmix.
2. Clone this repository:

   git clone https://github.com/CERC-Genomic-Medicine/RFMix2_local_ancesty.git
   cd RFMix2_local_ancesty
   

3. Download genetic maps zip file for build GRCh38 from https://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/ into Genetic_maps directory, unzip and re-format:

   mkdir Genetic_maps
   cd Genetic_maps
   wget https://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/plink.GRCh38.map.zip
   unzip plink.GRCh38.map.zip
   for i in {1..22}; do awk '{print "chr"$1,$4,$3}' OFS='\t' plink.chr${i}.GRCh38.map > chr${i}.GRCh38.map; done
   cd ..
   

4. Edit the nextflow.config file accordingly.
5. Load bcftools and nextflow modules:

   module load bcftools
   module load nextflow
   

6. Load your Python 3 virtual environment and make sure that Pandas is installed.
7. Run nextflow e.g.:

   nextflow run Pipeline.nf