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whatshap-software

WhatsHap

WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.

Information

Usage

See which versions of whatshap are available:

$ module avail whatshap

Load one version into your environment and run it:

$ module load whatshap/0.16
$ whatshap

Installation

Notes from the sysadmin during installation:

$ cd /tmp
$ module load python/3.6.2
$ sudo mkdir -p /export/apps/whatshap/0.16
$ sudo chown aorth:aorth /export/apps/whatshap/0.16
$ python -m venv /export/apps/whatshap/0.16
$ . /export/apps/whatshap/0.16/bin/activate
$ pip3 install whatshap
$ sudo chown -R root:root /export/apps/whatshap
whatshap-software.txt · Last modified: 2018/06/27 13:39 by aorth