Repository files navigation

VCF2Dis: an ultra-fast and efficient tool to calculate pairwise genetic distance and construct population phylogeny from VCF files

TheVCF2Dis article has been published inGigaScience, please cited this article if possible
Acceptance Date :2025 Mar 5
Publication :GigaScience
Title : VCF2Dis: an ultra-fast and efficient tool to calculate pairwise genetic distance and construct population phylogeny from VCF files
Doi :https://doi.org/10.1093/gigascience/giaf032

• 1. Install

Thenew version will be updated and maintained inhewm2008/VCF2Dis, please click below Link to download the latest version

hewm2008/VCF2Dis

Justsh make.sh to compile. The executableVCF2Dis can be found in the folder ofbin/VCF2Dis
ForLinux /Unix andmacOS

        tar -zxvf  VCF2DisXXX.tar.gz            # if Link do not work ,Tryre-install [zlib]library        cd VCF2DisXXX;                          # [zlib] and copy them to the library Dir        sh make.sh;                             # VCF2Dis-xx/src/include/zlib        ./bin/VCF2Dis

Note: If fail to link,try tore-install the librarieszlib
Note::R withape,dplyr andggtree are recommended

You can use Docker to install and run VCF2Dis. Follow the steps below:

1. Install Docker: Ensure Docker is installed on your system. If not, you can install it by following theDocker Official Documentation.
2. Pull the Docker Image: Use the following command to pull the VCF2Dis Docker image from the Alibaba Cloud Container Registry:

   docker pull registry.cn-shenzhen.aliyuncs.com/knight134/vcf2dis:v1.53e##  Docker image from the Alibaba Cloud Container Registrydocker run -it --rm vcf2dis:v1.53e VCF2Dis## After pulling the image, you can run the containe

1. Install Singularity: Ensure Singularity is installed on your system. If not, you can install it by following theSingularity Official Documentation.
2. Build the SIF File: Use the following command to build a Singularity image file (SIF) from the Docker image:

   singularity build vcf2dis_1.53e.sif docker://registry.cn-shenzhen.aliyuncs.com/knight134/vcf2dis:v1.53e# you can download followssingularityexec  vcf2dis_1.53e.sif  VCF2Dis

3. Download the SIF File:Alternatively, you can download the built SIF file directly from thevcf2dis_1.53e.sif. Once downloaded, you can run it using Singularity.

• 2. Main parameter description:

Usage: VCF2Dis -InPut<in.vcf>  -OutPut<p_dis.mat>-InPut<str>     Input one or muti GATK VCF genotype File-OutPut<str>     OutPut Sample p-Distance matrix-InList<str>     Input GATK muti-chr VCF Path List-SubPop<str>     SubGroup SampleList of VCF File [ALLsample]-Rand<float>   Probability (0-1]for each site to join Calculation [1]-help                Show morehelp [hewm2008 v1.53s]

For more details, please use-help and see theexample

-InFormat<str>   Input File is [VCF/FA/PHY] Format,defaut: [VCF]-InSampleGroup<str>   InFile of sample Group info,format(sample groupA)-TreeMethod<int>   Construct Tree Method,1:NJ-tree 2:UPGMA-tree [1]-KeepMF                Keep the Middle File diff& Use matrix

Three examples were provided in the directory ofexample/Example*

• 1. To Create the p_distance matrix and construct nj-tree newick tree

# 1.1) To new all the sample p_distance matrix and newick tree based VCF, run VCF2Dis directly      ./bin/VCF2Dis-InPutin.vcf.gz-OutPut p_dis.mat      #  ./bin/VCF2Dis     -InPut  in.fa.gz-OutPut p_dis.mat -InFormat  FA# 2.2) To new sub group sample p_distance matrix and and newick tree ; put their sample name into File sample.list      ./bin/VCF2Dis-InPutchr1.vcf.gz chr2.vcf.gz-OutPut p_dis.mat  -SubPop  sample.list

• 2. Simple tree visualization (for advanced tree display and annotation please refer toiTOL,Evolview,MEGA)
     you will obtain thep_dis.nwk tree file and neighbor-joining tree in pdf formatp_dis.pdf after VCF2Dis.

Note::if you can't get thep_dis.nwk tree file but had thep_dis.mat, here are the3 methods to get the tree file.

• 1. Running multiple times by using a method of sampling with replacement.Users can randomly select a part of the sites [-Rand] and construct a new nj-tree as above, and Repeat NN times [recommand NN=100]. X=(1,2....NN);

#!/bin/bashNN=100if ["$#"-eq  1 ];thenNN=$1fiforXin$(seq 1$NN)do./bin/VCF2Dis -InPut in.vcf.gz -OutPut p_dis_${X}.mat -Rand 0.25# PHYLIPNEW-3.69.650/bin/fneighbor -datafile p_dis_${X}.mat -outfile tree.out1_${X}.txt -matrixtype s -treetype n -outtreefile tree.out2_${X}.tredone

• 2. Merge all the nj-tree and construct and display a boostrap nj-tree. (For advanced display tree and annotation please refer toiTOL,Evolview andMEGA)

#!/bin/bashNN=100if ["$#"-eq  1 ];then  NN=$1ficat  p_*.nwk>    alltree_merge.tre#  cat  tree*.tre  > alltree_merge.trePHYLIPNEW-3.69.650/bin/fconsense   -intreefile   alltree_merge.tre  -outfile out  -treeprint Yperl  ./bin/percentageboostrapTree.pl    alltree_merge.treefile$NN    Final_boostrap.tre# NN is the input number

How to Install PHYLIPNEW please Click onhere or Click onhere(Chinese)

The formula for calculating p-distance between indivisuals from VCF SNP datasets was listed below:

            D_ij=(1/L) * [(sum(d(l)_ij))]

Where L is the length of regions where SNPs can be identified, and given the alleles at positionl are A/C between samplei and samplej:

            d(l)_ij=0.0     if the genotypes of the two individuals were AA and AA;            d(l)_ij=0.5     if the genotypes of the two individuals were AA and AC;            d(l)_ij=0.0     if the genotypes of the two individuals were AC and AC;            d(l)_ij=1.0     if the genotypes of the two individuals were AA and CC;            d(l)_ij=0.0     if the genotypes of the two individuals were CC and CC;

To further know about the p_distance matrix based the VCF file, please refer tothis website.

VCF2Dis have been cited in more than 170 times bysearching against google scholar.
Below were some NJ-tree images that I draw in the paper before.

• 50 Rices NBT
• 31 soybeans NG
  Display tree by MAGA after test Data VCF2Dis -i ALL.chr*.genotypes.vcf.gz -SubPop subsample203.list -InSampleGroup pop.info

• 📧hewm2008@gmail.com /hewm2008@qq.com /
• join the QQ Group : 125293663
• other Contributors ： Lian Xu (xulian@ntu.edu.cn); Xun Liao (1911751806@qq.com）

######################swimming in the sky and flying in the sea ########################### ##