Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

BCFtools/csq: Haplotype-aware variant consequences

View ORCID ProfilePetr Danecek, Shane A. McCarthy
doi: https://doi.org/10.1101/090811
Petr Danecek
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Petr Danecek
Shane A. McCarthy
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Motivation: Prediction of functional variant consequences is an important part of sequencing pipelines, allowing the categorization and prioritization of genetic variants for follow up analysis. However, current predictors analyze variants as isolated events, which can lead to incorrect predictions when adjacent variants alter the same codon, or when a frame-shifting indel is followed by a frame-restoring indel. Exploiting known haplotype information when making consequence predictions can resolve these issues.

Results: BCFtools/csq is a fast program for haplotype-aware consequence calling which can take into account known phase. Consequence predictions are changed for 2839 of 4934 compound variants found in the 81.7M variants in the 1000 Genomes Project data, with an average of 139 compound variants per haplotype. Predictions match existing tools when run in localized mode, but the program is an order of magnitude faster and requires an order of magnitude less memory.

Availability: The program is freely available for commercial and non-commercial use in the BCFtools package which is available for download from http://samtools.github.io/bcftools

Contact: pd3{at}sanger.ac.uk

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
Back to top
PreviousNext
Posted December 01, 2016.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
BCFtools/csq: Haplotype-aware variant consequences
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
BCFtools/csq: Haplotype-aware variant consequences
Petr Danecek, Shane A. McCarthy
bioRxiv 090811; doi: https://doi.org/10.1101/090811
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
BCFtools/csq: Haplotype-aware variant consequences
Petr Danecek, Shane A. McCarthy
bioRxiv 090811; doi: https://doi.org/10.1101/090811

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4382)
  • Biochemistry (9591)
  • Bioengineering (7090)
  • Bioinformatics (24856)
  • Biophysics (12600)
  • Cancer Biology (9955)
  • Cell Biology (14349)
  • Clinical Trials (138)
  • Developmental Biology (7948)
  • Ecology (12105)
  • Epidemiology (2067)
  • Evolutionary Biology (15988)
  • Genetics (10925)
  • Genomics (14738)
  • Immunology (9869)
  • Microbiology (23659)
  • Molecular Biology (9484)
  • Neuroscience (50855)
  • Paleontology (369)
  • Pathology (1539)
  • Pharmacology and Toxicology (2681)
  • Physiology (4013)
  • Plant Biology (8657)
  • Scientific Communication and Education (1508)
  • Synthetic Biology (2394)
  • Systems Biology (6433)
  • Zoology (1346)