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Related Concept Videos

Genetic Variation01:25

Genetic Variation

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Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles,...
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CompoundHetVIP: Compound Heterozygous Variant Identification Pipeline.

Dustin B Miller1, Stephen R Piccolo1

  • 1Department of Biology, Brigham Young University, Provo, UT, 84602, USA.

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|March 9, 2021
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Summary
This summary is machine-generated.

Compound Heterozygous Variant Identification Pipeline (CompoundHetVIP) simplifies identifying genetic variants by packaging tools into a Docker image. This pipeline aids in discovering missing heritability for human diseases and phenotypes.

Keywords:
Geneticscompound heterozygousgenome analysisphasingreproducibilitytrio

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Area of Science:

  • Genetics
  • Bioinformatics
  • Computational Biology

Background:

  • Identifying compound heterozygous (CH) variants is crucial for genetic research.
  • Existing computational tools present challenges in installation, dependencies, and file formatting.

Purpose of the Study:

  • To develop a streamlined computational pipeline for compound heterozygous variant identification.
  • To simplify the process of analyzing genomic data for CH, homozygous alternate, and de novo variants.

Main Methods:

  • Developed Compound Heterozygous Variant Identification Pipeline (CompoundHetVIP) using a Docker image.
  • Encapsulated tools for file aggregation, liftover, genotyping, phasing, normalization, annotation, and variant identification.
  • Applied the pipeline to a publicly available trio dataset.

Main Results:

  • Successfully identified candidate CH and homozygous alternate variants in genes.
  • Demonstrated the pipeline's utility on whole-genome, whole-exome, or targeted exome sequencing data.
  • The pipeline produced analysis-ready output files for further evaluation.

Conclusions:

  • CompoundHetVIP overcomes common computational challenges in variant identification.
  • The pipeline facilitates the discovery of genetic variants contributing to human diseases and phenotypes.
  • CompoundHetVIP is open-source, promoting accessibility for researchers.