Reasons:
I want ot use snp microarray data to built a phylogenetic tree. I did some google search, and found out [SNPhylo](http://chibba.pgml.uga.edu/snphylo/) can achieve this goal. But it requires Hapmap file format.
What I have are Geno.bed, Geno.bim and Geno.fam, the binary Plink format. if you have Geno.ped and Geno.map files, it will work the same way.
The solution is proposed by Pablo Marin-Garcia from the Biostar Forum Question.
For converting ped to HapMap I convert first to tped with plink, and I used plink1.9:
plink --bfile Geno --recode transpose --out GenoT
PLINK v1.90b4 64-bit (20 Mar 2017) www.cog-genomics.org/plink/1.9/
(C) 2005-2017 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to GenoT.log.
Options in effect:
--bfile Geno
--out GenoT
--recode transpose
8703 MB RAM detected; reserving 4351 MB for main workspace.
301746 variants loaded from .bim file.
42 people (40 males, 2 females) loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 42 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.987983.
301746 variants and 42 people pass filters and QC.
Note: No phenotypes present.
--recode transpose to GenoT.tped + GenoT.tfam ... done.
And then his perl script convert_tped_to_hapmap.pl.
perl convert_tped_to_hapamp.pl --tped GenoT.tped --tfam GenoT.tfam --build=ncbi_36
== LOG conversion ped to hapmap ==
Started at: Mon Aug 19 11:30:43 2019
hapmap file : GenoT.tped.hapmap
tped file : GenoT.tped
tfam file : GenoT.tfam
map file :
pheno file :
#[MSG] loading tfam file 'GenoT.tfam'
...end. 42 lines processed
#[MSG] processing tped file 'GenoT.tped'.
...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ENDED at: Mon Aug 19 11:31:19 2019
== END ==
Then, you will get GenoT.tped.hapmap file.
The installation of SNPhylo on my Ubuntu 16.06 is a little bit different from the manual, but it worked for me. If you encounter the same situation, please follow my steps.
- Install the R (if R is not installed; as root)
apt-get -y install r-base-dev r-cran-getopt r-cran-rgl
My R version: 3.6.1 (2019-07-05)
- Make a SNPhylo directory in your home directory
echo ${HOME}
/home/mianlee
SNPHYLO_HOME="/home/mianlee/snphylo"
mkdir -p "${SNPHYLO_HOME}/bin"
- Install the MUSCLE (if MUSCLE is not installed)
curl -O http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz
tar xvfz muscle3.8.31_i86linux64.tar.gz -C "${SNPHYLO_HOME}/bin"
ln -sf "${SNPHYLO_HOME}/bin/muscle3.8.31_i86linux64" "${SNPHYLO_HOME}/bin/muscle"
- Install the Phylip package (if Phylip package is not installed)
I downloaded phylip-3.697
tar xvfz phylip-3.697.tar.gz -C "${SNPHYLO_HOME}"
ln -sf "${SNPHYLO_HOME}/phylip-3.697" "${SNPHYLO_HOME}/phylip"
pushd "${SNPHYLO_HOME}/phylip/src"
cp Makefile.unx Makefile
make install
popd
5.Intall R packages: gdsfmt, SNPRelate, getopt,igraph and phangorn.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("gdsfmt")
BiocManager::install("SNPRelate")
install.packages("getopt")
# Install libgfortran.so.4 on ubuntu 16.06
sudo add-apt-repository ppa:jonathonf/gcc-7.1
sudo apt-get update
sudo apt-get install gcc-7 g++-7
sudo apt-get install gfortran-7
install.packages("igraph")
install.packages("phangorn")
- Install the SNPhylo
curl -O http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz
tar xvfz snphylo.tar.gz -C "${SNPHYLO_HOME}"
- Setup the SNPhylo
$ pushd "${SNPHYLO_HOME}/SNPhylo"
$ bash setup.sh
START TO SET UP FOR SNPHYLO!!!
The detected path of Rscript is /bin/Rscript. Is it correct? [Y/n] y
The detected path of python is /bin/python. Is it correct? [Y/n] y
muscle is not found. Is the program already installed? [y/N] y
Please enter the path of muscle program (ex: /home/foo/bin/muscle): /home/foo/snphylo/bin/muscle
dnaml is not found. Is the program already installed? [y/N] y
Please enter the path of dnaml program (ex: /home/foo/bin/dnaml): /home/foo/snphylo/phylip/exe/dnaml
At least one R package (gdsfmt, SNPRelate, getopt or phangorn) to run this pipeline is not found. Are the packages already installed? [y/N]
Do you want to install the packages by this script? [y/N] y
...... (Installing R packages)
SNPHYLO is successfully installed!!!
$ popd
For other operating system, see SNPhylo homepage.
SNPhylo doesn't work with python3, so I use python2 instead of python3 to set up "bash setup.sh" again.
./snphylo.sh -H ~/Desktop/NatGeo/GenoT.tped.hapmap