Table 5 Software components of the pipeline.

vt

Decomposition and Normalization of Variants

v0.57721

https://genome.sph.umich.edu/wiki/Vt

Variant Effect Predictor (VEP)

Variant Annotation

v84

http://www.ensembl.org/info/docs/tools/vep/script/index.html

GEMINI

Storage of annotated variants

0.30.1

https://github.com/arq5x/gemini

OMIM API

Retrieval and linkage of OMIM terms to causative genes

As accessed on 28/06/19

https://www.omim.org/api

Phenolyzer

Linkage of HPO terms to causative genes

v1.0.5

http://phenolyzer.wglab.org

Phenoparser

Process and storage of OMIM and Phenolyzer results and generation of gene panels

v1.0.0

https://github.com/TimoLassmann/Phenoparser

BCFtools

Manipulation of variant data files

v1.6

http://www.htslib.org/download

HTSlib (includes tabix and bgzip)

Indexing variant data files

v1.6

http://www.htslib.org/download

Grabix

Indexing variant data files

0.1.8

https://github.com/arq5x/grabix

R

Collation of data and generation of patient report files

3.2.3

https://www.r-project.org