SHAPEIT 2.r900

SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.

SHAPEIT has several notable features:

- Linear complexity with the number of SNPs and conditioning haplotypes.
- Whole chromosome GWAS scale datasets can be phased in a single run.
- Phasing individuals with any level of relatedness.
- Phasing is multi-threaded to tailor computational times to your resources.
- Handles X chromosomes phasing.
- Phasing using a reference panel (eg.1,000 Genomes) to aid phasing.
- Ideal for pre-phasing imputation together with IMPUTE2.

Accessing the software

To load the module:

$ module load SHAPEIT/2.r900.glibcv2.12

An example command to include in your job script:

$ shapeit --input-bed <input_bed_files> \
        --input-map <input_map files> \
        --output-max <output_files> \
        --thread <number_of_threads>

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

Previous versions of this application are recorded below:

  • SHAPEIT 2.r837

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the website for more information about this application.


Last modified: 14 March 2018