VCF2Dis: A new simple and efficient software to calculate p-distance matrix based Variant Call Format
Just [make] or [sh make.sh ] to compile this software.the final software can be found in the Dir [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
make ; make clean # VCF2Dis-xx/src/include/zlib
./bin/VCF2Dis
Note: If fail to link,try to re-install the libraries zlib
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- Parameter description:
Usage: VCF2Dis -InPut <in.vcf> -OutPut <p_dis.mat>
-InPut <str> Input GATK VCF genotype File
-OutPut <str> OutPut Sample p-Distance matrix
-SubPop <str> SubGroup SampleList of VCFFile [ALLsample]
-KeepMF Keep the Middle File diff & Use matrix
-help Show more help [hewm2008 v1.10]-
- To Create the p_distance matrix
# 2.1) To new all the sample p_distance matrix based VCF, run VCF2Dis directly
./bin/VCF2Dis -InPut in.vcf.gz -OutPut p_dis.mat
# 2.2) To new sub group sample p_distance matrix ; put their sample name into File sample.list
./bin/VCF2Dis -InPut in.vcf.gz -OutPut p_dis.mat -SubPop sample.list
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- construct nj-tree and present it (need deal with Other software)
# 3.1 Run PHYLIP
# After p_distance done , software PHYLIP 3.69 (http://evolution.genetics.washington.edu/phylip.html) ,with neighbor-joining method can was used to construct the phylogenetic tree on the basis of this p_distance matrix;
PHYLIPNEW-3.69.650/bin/fneighbor -datafile p_dis.matrix -outfile tree.out1.txt -matrixtype s -treetype n -outtreefile tree.out2.tre
# 3.2 Run MEGA
# The MEGA6 (http://www.megasoftware.net/) was used to present the phylogenetic tree based this file [tree.out2.tre]
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- you can see the neighbor-joining tree and save it as PDF format
To new the p_distance matrix besed the VCF file. the more infomation about the p_distance matrix, see this website. The VCF SNPs datasets were used to calculate p-distance between individuals, according to the follow formula to operate the sample i and sample j genetic distance:
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:
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;
some NJ-tree images which I draw in the paper before.
- 📧 hewm2008@gmail.com / hewm2008@qq.com
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