CRwiki

GLIMPSE2 is a set of tools for low-coverage whole genome sequencing imputation. GLIMPSE2 is based on the GLIMPSE model and designed for reference panels containing hundreads of thousands of reference samples, with a special focus on rare variants.

• GLIMPSE2_chunk splits the genome into chunks for imputation and phasing
• GLIMPSE2_split_reference creates the reference panel representation used by GLIMPSE2_phase. It allows major speedups for large reference panels.
• GLIMPSE2_phase program to impute and phase low coverage sequencing data
• GLIMPSE2_ligate concatenates phased chunks of data into chromosome-wide phased files

If you use GLIMPSE in your research work, please cite the following papers more.

Bellow description covers preparation and compilation of GLIMPSE2_phase v2.0.0 ¹⁾

Login to anthill23, and download required sources ²⁾

mkdir -p ~/anthill23_soft/glimpse

cd ~/anthill23_soft/glimpse
git clone https://github.com/samtools/htslib htslib_src
cd htslib_src
git submodule update --init --recursive

cd ~/anthill23_soft/glimpse
wget https://boostorg.jfrog.io/artifactory/main/release/1.73.0/source/boost_1_73_0.tar.bz2
tar --bzip2 -xf boost_1_73_0.tar.bz2

cd ~/anthill23_soft/glimpse
git clone https://github.com/odelaneau/glimpse.git

start interactive session in which download and compile htslib, boost, glimpse2_phase ³⁾:

@anthill23:~$ srun --cpus-per-task 8 --mem-per-cpu 20G  -J glimpse_prep --partition=medium --pty --preserve-env bash

compile htslib ⁴⁾:

cd ~/anthill23_soft/glimpse/htslib_src
autoreconf -i
./configure --enable-libcurl --prefix=/home/users/${USER}/anthill23_soft/glimpse/htslib
make
make install

compile boost ⁵⁾:

cd ~/anthill23_soft/glimpse/boost_1_73_0
./bootstrap.sh --with-libraries=iostreams,program_options,serialization --prefix=../boost
./b2 install

compile GLIMPSE2_phase ⁶⁾:

cd ~/anthill23_soft/glimpse/glimpse/phase
sed -i 's/desktop: HTSSRC.*/desktop: HTSSRC=\/home\/users\/${USER}\/anthill23_soft\/glimpse\/htslib/' makefile
sed -i 's/desktop: HTSLIB_INC.*/desktop: HTSLIB_INC=\$(HTSSRC)\/include/' makefile
sed -i 's/desktop: HTSLIB_LIB.*/desktop: HTSLIB_LIB=\$(HTSSRC)\/lib\/libhts.a/' makefile
sed -i 's/desktop: BOOST_INC.*/desktop: BOOST_INC=\/home\/users\/${USER}\/anthill23_soft\/glimpse\/boost\/include/' makefile
sed -i 's/desktop: BOOST_LIB_IO.*/desktop: BOOST_LIB_IO=\/home\/users\/${USER}\/anthill23_soft\/glimpse\/boost\/lib\/libboost_iostreams.a/' makefile
sed -i 's/desktop: BOOST_LIB_PO.*/desktop: BOOST_LIB_PO=\/home\/users\/${USER}\/anthill23_soft\/glimpse\/boost\/lib\/libboost_program_options.a/' makefile
sed -i 's/desktop: BOOST_LIB_SE.*/desktop: BOOST_LIB_SE=\/home\/users\/${USER}\/anthill23_soft\/glimpse\/boost\/lib\/libboost_serialization.a/' makefile
make desktop

compile GLIMPSE2_chunk / ligate / split_reference

#repeat the same as for GLIMPSE2_phase described above, but in different folder
cd ~/anthill23_soft/glimpse/glimpse/chunk           # for GLIMPSE2_chunk
cd ~/anthill23_soft/glimpse/glimpse/ligate          # for GLIMPSE2_ligate
cd ~/anthill23_soft/glimpse/glimpse/split_reference # for GLIMPSE2_split_reference

test created binary, you should get similar output :

cd ~/anthill23_soft/glimpse/glimpse/phase
./bin/GLIMPSE2_phase 

[GLIMPSE2] Phase and impute low coverage sequencing data
  * Authors              : Simone RUBINACCI & Olivier DELANEAU, University of Lausanne
  * Contact              : simone.rubinacci@unil.ch & olivier.delaneau@unil.ch
  * Version              : GLIMPSE2_phase v2.0.0 / commit = 0fcf590 / release = 2023-10-09
  * Citation             : BiorXiv, (2022). DOI: https://doi.org/10.1101/2022.11.28.518213
  *                      : Nature Genetics 53, 120–126 (2021). DOI: https://doi.org/10.1038/s41588-020-00756-0
  * Run date             : 05/11/2023 - 08:17:29

ERROR: You must specify input files using one of the following options: --bam, --bam-list or --input-gl

finish

#exit interactive mode when finished with exit command
exit

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