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A suite of perl modules that compares genomic variations with reference genome annotations and generates the possible effects each variant may have on the transcripts it overlaps. VAGrENT evaluates each variation/transcript combination and describes the effects in the mRNA, CDS and protein sequence contexts. It provides details of the sequence and position of the change within the transcript/protein as well as Sequence Ontology terms to classify its consequences.

Software type:
Package
Interface:
Command line interface
Restrictions to use:
None
Operating system:
Unix/Linux
Programming languages:
Perl
Computer skills:
Advanced
Stability:
Stable
Requirements:
Samtools, tabix, vcftools
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Maintainer

  • VAGrENT <cgpit at sanger.ac.uk>
  • Animals
    • Homo sapiens

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