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. 
Python, wget
Internet connection during installation (for downloading and extracting hg19 reference genome).
Data storage: For installation we recommend a storage capacity of > 10 GB. 

Installation

1. Install dependencies, you can skip this step if these packages are already installed on your system

        apt-get install python3.6            
        apt-get install mawk
        apt-get install p7zip-full
        apt-get install bwa
   

   SAMtools: We recommend the newests versions of SAMtools (e.g. > 1.4.1)

        1. wget https://github.com/samtools/samtools/releases/download/1.4.1/samtools-1.4.1.tar.bz2 -O samtools.tar.bz2
        2. tar -xjvf samtools.tar.bz2 
        3. cd samtools-1.4.1/
        4. ./configure
        5. make
        6. make install
   

Usage and examples

Yleaf: FASTQ (raw reads)

python Yleaf.py -fastq raw_reads.fastq -out out -f [reference.fasta] -pos Position_files/[hg19.txt-hg38.txt] -r 1 -q 20 -b 90 -t 16 

Yleaf: BAM format

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

Haplogroup prediction (w/output generated from Yleaf)

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

3. See complete manual at the website: https://www.erasmusmc.nl/genetic_identification/resources/

4. Bug report

Please send an email at [email protected] if there is a problem getting the software up and running.

References and Supporting Information

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

https://doi.org/10.1093/molbev/msy032