Yleaf: software for human Y-chromosomal haplogroup inference from next generation sequencing data

Arwin Ralf, Diego Montiel Gonzalez, Kaiyin Zhong and Manfred Kayser

Department of Genetic Identification

Erasmus MC University Medical Centre Rotterdam, The Netherlands

Requirements

Operating system: Linux only. Tested on Ubuntu 16.04LTS, but should also work on newer version of Ubuntu. It should be easy to made it work on other Linux distributions. 
Python3 with pandas >= 0.23.0 and numpy >= 1.14.3
Internet connection during installation (for downloading and extracting hg19/hg38 reference genome).
Data storage: For installation we recommend a storage capacity of > 10 GB.

Installation

You can either build a conda environment with all dependencies

# create the conda environment
conda create --name yleaf_env python=3.6
# activat the environment
conda activate yleaf_env
# install required python libraries
conda install pandas
conda install numpy
# install Burrows-Wheeler Aligner for fastQ files
conda install -c bioconda bwa
# install SAMtools
conda install -c bioconda samtools
# clone the yleaf repository
git clone https://github.com/genid/Yleaf.git

# finally if you want to use FASTQ files use the provided install.py
script to download required genome data
cd Yleaf
python install.py

or manually install everything

# install python and libraries
apt-get install python3.6
pip3 install pandas
pip3 install numpy
# install Burrows-Wheeler Aligner for FASTQ files
sudo apt-get install bwa
# install SAMtools
wget https://github.com/samtools/samtools/releases/download/1.4.1/
samtools-1.4.1.tar.bz2 -O samtools.tar.bz2
tar -xjvf samtools.tar.bz2 3. 
cd samtools-1.4.1/
./configure 5. make
make install
# clone the yleaf repository
git clone https://github.com/genid/Yleaf.git

# finally if you want to use FASTQ files use the provided install.py
script to download required genome data
cd Yleaf
python install.py

Usage and examples

In version 3.0 we switched to using YFull (v10.01) for the underlying tree structure of the haplogroups. This also means that predictions are a bit different compared to earlier versions.

Yleaf: FASTQ (raw reads)

python Yleaf.py -fastq raw_reads.fastq -f reference_indexed/genome.fasta -pos Position_files/new_position_files/[hg19.txt/hg38.txt] -out out -r 1 -q 20 -b 90 -t 4

Yleaf: BAM or CRAM format

python Yleaf.py -bam file.bam -pos Position_files/new_position_files/[hg19.txt/hg38.txt] -out out -r 1 -q 20 -b 90 

python Yleaf.py -cram file.cram -pos Position_files/new_position_files/[hg19.txt/hg38.txt] -out out -r 1 -q 20 -b 90  -f genome.fasta

Haplogroup prediction (w/output generated from Yleaf)

python predict_haplogroup.py -input Output_files/ -out output.hg

Additional information

For a more comprehensive manual please have a look at the yleaf_manual.

If you have a bug to report or a question about installation consider sending an email to b.vanwersch at erasmusmc.nl or create an issue on GitHub.

References and Supporting Information

A. Ralf, et al., Yleaf: software for human Y-chromosomal haplogroup inference from next generation sequencing data (2018).

https://academic.oup.com/mbe/article/35/5/1291/4922696

teepean / Yleaf