RegTools commands

To get a list of all available regtools commands regtools --help

The main regtools commands are

• cis-splice-effects
• junctions
• variants

cis-splice-effects

This set of tools helps identify and work with aberrant splicing events near variants, these could be somatic variants or germline polymorphisms/mutations. These variants are hypothesized to act in cis and affect how the gene is transcribed.

Below are links to detailed explanations of the cis-splice-effects sub-commands:

• identify
• associate

cis-ase

This set of tools helps identify and work with allele-specific-expression near variants, these could be somatic variants or germline polymorphisms/mutations. These variants are hypothesized to act in cis and affect how the gene is transcribed.

Below are links to detailed explanations of the cis-ase sub-commands:

• identify

junctions

The transcriptome structure is often summarized from a RNAseq experiment with a BED file. This BED file contains the exon-exon boundary co-ordinates which are referred to as junctions. For example, TopHat outputs a file called 'junctions.bed' which contains this information. This file is very useful if you are interested in studying which exons/transcripts are expressed, splicing effects etc. On the command line these commands can be accessed using the regtools junctions command.

Listed below are links to detailed explanations of the junctions sub-commands:

• extract
• annotate

variants

The variants sub-command contains a list of tools that deal with variants that are potentially regulatory in nature. Variants are generally accepted in the standard VCF format unless specified otherwise.

Below are links to detailed explanations of the variants sub-commands:

• annotate