From listmaster animalgenome.org Wed Feb 17 10:06:34 2021
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From: "Abasht, Behnam" <abashtudel.edu>
Postmaster: submission approved by list moderator
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: VADT: New tool for allelic expression analysis
Date: Wed, 17 Feb 2021 10:06:34 -0600
I am pleased to announce the release of VADT (VCF ASE Detection Tool), a
new tool for allelic expression analysis. Primarily written by Joe
Tomlinson as a part of his MS thesis in Bioinformatics in my laboratory,
VADT is a streamlined analysis tool for the detection of allele-specific
expression (ASE) from RNA-seq data. Specifically, VADT takes in a VCF file,
filters the data, performs a binomial test on all biallelic samples,
controls for the false discovery rate, and finally reports back all the
significant findings. What makes VADT especially unique is that the program
implements two different statistical methods for ASE detection:
(i) Detection of ASE variants across multiple samples: a meta-analysis to
identify significant ASE variants across multiple samples.
(ii) Detection of ASE samples among multiple samples: a multi-dimensional
p-value adjustment to identify ASE samples among multiple samples.
The entire process is streamlined into one python script that can easily be
run on an HPC system using a parameter file or through the HPC environment.
The paper implementing VADT titled Investigation of Allele Specific
Expression in Various Tissues of Broiler Chickens Using the Detection Tool
VADT is now available online ( https://rdcu.be/cfny0). The paper goes into
extensive details about the biological interpretations of the results,
which should also assist researchers in their own ASE studies.
The full program can be found at the following location
https://github.com/mjtiv/VADT with example test data and output for a user
to try and demo the program.
We greatly appreciate all feedback and suggestions with the program!
--
Behnam Abasht
Associate Professor
Department of Animal and Food Sciences, University of Delaware
531 S. College Ave., 035 Townsend Hall, Newark, DE 19716
Phone: 302-831-8876 (office), Fax: 302-831-2822
Email: abashtUDel.edu
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