VCF2Dis

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

1) Install and Parameter

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• 1. Install

The new version will be updated and maintained in hewm2008/VCF2Dis, please click below Link to download the latest version

hewm2008/VCF2Dis

Download

Option 1 : Local compilation

Just sh make.sh to compile. The executable VCF2Dis can be found in the folder of bin/VCF2Dis
For Linux /Unix and macOS

        tar -zxvf  VCF2DisXXX.tar.gz            # if Link do not work ,Try re-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 to re-install the libraries zlib
Note:: R with ape, dplyr and ggtree are recommended

Option 2: Docker container

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 the Docker 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 Registry
   docker run -it --rm vcf2dis:v1.53e VCF2Dis                                ## After pulling the image, you can run the containe

Option 3: Singularity container

1. Install Singularity: Ensure Singularity is installed on your system. If not, you can install it by following the Singularity 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 follows 
   singularity exec  vcf2dis_1.53e.sif  VCF2Dis

3. Download the SIF File:Alternatively, you can download the built SIF file directly from the vcf2dis_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 more help [hewm2008 v1.53s]

For more details, please use -help and see the example

		-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

2) Example

Three examples were provided in the directory of example/Example*

1) an Example of nj-tree with no boostrap

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• 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	-InPut	in.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	-InPut	chr1.vcf.gz chr2.vcf.gz	-OutPut p_dis.mat  -SubPop  sample.list

• 2. Simple tree visualization (for advanced tree display and annotation please refer to iTOL, Evolview, MEGA)
     you will obtain the p_dis.nwk tree file and neighbor-joining tree in pdf format p_dis.pdf after VCF2Dis.

Note::if you can't get the p_dis.nwk tree file but had the p_dis.mat, here are the 3 methods to get the tree file.

2) an Example of nj-tree with boostrap

• 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/bash
NN=100
if [ "$#"  -eq  1 ]; then
	NN=$1
fi
for X in $(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}.tre
done

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

#!/bin/bash
NN=100
if [ "$#"  -eq  1 ]; then
  NN=$1
fi

cat  p_*.nwk  >    alltree_merge.tre   #  cat  tree*.tre  > alltree_merge.tre
PHYLIPNEW-3.69.650/bin/fconsense   -intreefile   alltree_merge.tre  -outfile out  -treeprint Y
perl  ./bin/percentageboostrapTree.pl    alltree_merge.treefile    $NN    Final_boostrap.tre  # NN is the input number

How to Install PHYLIPNEW please Click on here or Click on here(Chinese)

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4) Introduction

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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 position l are A/C between sample i and sample j:

            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 to this website.

5) Results

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VCF2Dis have been cited in more than 170 times by searching 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

6) Discussing

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• 📧 hewm2008@gmail.com / hewm2008@qq.com
• join the QQ Group : 125293663

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