For more information please read this manuscript
Current release: v1.0.0. Release date: April 07, 2023
RESHAPE is available under a MIT license. For more information please see the LICENSE.
RESHAPE removes sample-level genetic information from a reference panel to create a synthetic reference panel. By providing it with a genetic map and the VCF/BCF of a reference panel, RESHAPE outputs a VCF/BCF of the same size where each haplotypes corresponds to a mosaic of the original haplotypes of the reference panel.
It takes as input:
- --vcf: reference panel in the VCF or BCF file format
- --region: chromosome to shuffle
- --output: output path for the synthetic reference panel (should be in VCF or BCF file format)
- --map: path to the recombination map
- --seed: the seed for the rng
- --gen: the number of generations (K in the paper) to simulate recombination events
And outputs a synthetic reference panel of the same size as the original reference panel in the VCF or BCF file format.
./bin/haploshuffling --vcf $INPUT_FILE --region $CHR --output $OUTPUT --map $MAP --seed 13524 --gen 100
Building from source requires a version of GCC > 4.4.
The following libraries are required:
- HTSlib version >= 1.7
- BOOST version >= 1.65
To install htslib:
wget https://github.com/samtools/htslib/releases/download/1.16/htslib-1.16.tar.bz2
tar -xf htslib-1.16.tar.bz2
mv htslib-1.16 htslib
cd htslib
autoheader; autoconf; ./configure; #optional
make
To install boost:
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 boost_1_73_0
./bootstrap.sh --with-libraries=iostreams,program_options,serialization --prefix=../boost #where ../boost is your custom boost installation prefix
./b2 install
cd ../boost #change this to the folder you used as --prefix for the bootstrap script
Make sure that the following standard library flags can be used by g++ on your system: -lz -lpthread -lbz2 -llzma -lcurl -lcrypto
The installation should take less than a minute once the other libraries are installed.
To test if the software is correctly installed you can run the tool on the example dataset: bash validation.sh. This test should take less than a minute.
Building from source is not necessary as we provide the static binary at the release link: https://github.com/TheoCavinato/RESHAPE/releases/
To obtain the docker container:
docker pull theocavinato/reshape
docker run -it theocavinato/reshape
Then, you can use reshape by using
haploshuffling_static