ILRI Research Computing

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====== 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 =====

  * Version: 0.16
  * Added: June, 2018
  * Link: https://whatshap.readthedocs.io/en/latest/index.html

===== Usage =====

See which versions of whatshap are available:
<code>$ module avail whatshap</code>

Load one version into your environment and run it:
<code>$ module load whatshap/0.16
$ whatshap</code>

===== Installation ======

Notes from the sysadmin during installation:

<code>$ 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</code>