LAUSR

About LAUSR
Donate
Contact Us

Follow us:

You are not signed in:

Sign Up!


   Articles with "variant call" as a keyword



Photo by akshar_dave from unsplash

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files

Sign Up to like & get
recommendations! Published in 2021 at "Briefings in bioinformatics"

DOI: 10.1093/bib/bbaa227

Abstract: The triangular correlation heatmap aiming to visualize the linkage disequilibrium (LD) pattern and haplotype block structure of SNPs is ubiquitous component of population-based genetic studies. However, current tools suffered from the problem of time and… read more here.

Keywords: variant call; format files; haplotype blocks; haplotype ... See more keywords
Photo by campaign_creators from unsplash

vcfr: a package to manipulate and visualize variant call format data in R

Sign Up to like & get
recommendations! Published in 2017 at "Molecular Ecology Resources"

DOI: 10.1111/1755-0998.12549

Abstract: Software to call single‐nucleotide polymorphisms or related genetic variants has converged on the variant call format (VCF) as the output format of choice. This has created a need for tools to work with VCF files.… read more here.

Keywords: package; variant call; format; call ... See more keywords
Photo by akshar_dave from unsplash

Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR.

Sign Up to like & get
recommendations! Published in 2022 at "F1000Research"

DOI: 10.12688/f1000research.109080.2

Abstract: In this opinion article, we discuss the formatting of files from (plant) genotyping studies, in particular the formatting of metadata in Variant Call Format (VCF) files. The flexibility of the VCF format specification facilitates its… read more here.

Keywords: call format; vcf; variant call; plant ... See more keywords
Photo by akshar_dave from unsplash

A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar

Sign Up to like & get
recommendations! Published in 2022 at "PLoS Computational Biology"

DOI: 10.1371/journal.pcbi.1009123

Abstract: Since its introduction in 2011 the variant call format (VCF) has been widely adopted for processing DNA and RNA variants in practically all population studies—as well as in somatic and germline mutation studies. The VCF… read more here.

Keywords: format; call format; vcf; variant call ... See more keywords