variant calling

Apr
14
Apr/14 09:00 - Apr/15 17:00
EDINBURGH GENOMICS The University of Edinburgh Ashworth Laboratories The King's Buildings Charlotte Auerbach Road Edinburgh EH9 3FL Scotland, United Kingdom

GATK Best Practices for Variant Discovery workshop

This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit (https://www.broadinstitute.org/gatk/), using the “Best Practices” developed by the GATK team. The workshop is composed of one day of lectures (including many opportunities for Q&A) and one optional day of hands-on training.

For more information and to register, please visit https://genomics.ed.ac.uk/gatk-best-practices-variant-discovery.

An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors

Background: Identification of one or several disease causing variant(s) from the large collection of variants present in an individual is often achieved by the sequential use of heuristic filters. The recent development of whole exome sequencing enrichment designs for several non-model species created the need for a species-independent, fast and versatile analysis tool, capable of tackling a wide variety of standard and more complex inheritance models. With this aim, we developed "Mendelian", an R-package that can be used for heuristic variant filtering.

VirVarSeq

For Illumina sequencing, single base substitutions are the main error source and impede powerful assessment of low-frequency mutations. Fortunately, base calls are complemented with quality scores (Qs) that are useful for differentiating errors from the real low-frequency mutations. The variant calling tool, Q-cpileup, exploits the Qs of nucleotides in a filtering strategy to increase specificity and is imbedded VirVarSeq, which allows variant calling starting from fastq files.

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