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glfMultiples specifications

Information


Unique identifier OMICS_00061
Name glfMultiples
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Input format GLF
Output data Variant calls.
Output format VCF
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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glfMultiples citations

 (7)
library_books

Analysis of single nucleotide polymorphisms based on RNA sequencing data of diverse bio geographical accessions in barley

2016
PMCID: 5018957
PMID: 27616653
DOI: 10.1038/srep33199

[…] sequence variations to elucidate on the diversity of the population., mapping rna-seq reads into the genomic framework of morex allowed identifying snps using the following programs: freebayes, glfmultiples, and samtools (). although each program yielded a distinct number of snps, we extracted those that were commonly called by all programs, as these were considered the accurate snps (). […]

library_books

Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery

2016
PMCID: 5019950
PMID: 27428751
DOI: 10.1038/ng.3592

[…] these genomic regions, leaving 32,967,859 bases under consideration (~1% of the human genome) within 17,800 genes., standard filters for variants that were called with posterior probability >99% (glfmultiples snp quality > 20), were at least 5 bp away from an indel detected in the 1000g pilot project, were targeted in at least 95% individuals and had a total depth across samples […]

library_books

Exome Sequencing of Phenotypic Extremes Identifies CAV2 and TMC6 as Interacting Modifiers of Chronic Pseudomonas aeruginosa Infection in Cystic Fibrosis

2015
PMCID: 4457883
PMID: 26047157
DOI: 10.1371/journal.pgen.1005273

[…] likelihoods for exome targeted regions and 50 flanking bases, accounting for per base alignment quality (baq) using samtools []. variable sites and their allele frequencies were identified using glfmultiples, and a support vector machine (svm) classifier was used flag probable false-positive variant sites. snvs at hapmap polymorphic sites and omni 2.5 array polymorphic sites in the 1000 […]

library_books

Detection of phylogenetically informative polymorphisms in the entire euchromatic portion of human Y chromosome from a Sardinian sample

2015
PMCID: 4423141
PMID: 25926048
DOI: 10.1186/s13104-015-1130-z

[…] : table s1 (sheet 4) shows the conversion key of the sample numbering between the two datasets., sequence alignment was performed with bwa-0.5.9 [], and variant calling with a modified version of glfmultiples [] as described in []., a more strict mapping quality filtering (requiring 60 in the phred scale, which means that both reads in a ngs read pair were aligned with no ambiguity) […]

library_books

Comparing variant calling algorithms for target exon sequencing in a large sample

2015
PMCID: 4359451
PMID: 25884587
DOI: 10.1186/s12859-015-0489-0

[…] site in hardy-weinberg equilibrium. these allele frequency priors combine with the likelihoods calculated per individual to generate posterior genotype probabilities. we used the pbc implemented as glfmultiples (http://genome.sph.umich.edu/wiki/glfmultiples), which also generated variant calls for nhlbi go exome sequencing project (esp) and contributed to 1000 genomes project analyses [,,]., […]

library_books

Variant calling in low coverage whole genome sequencing of a Native American population sample

2014
PMCID: 3914019
PMID: 24479562
DOI: 10.1186/1471-2164-15-85

[…] using the beagle haplotypes as input. specifically, samtools-hybrid is used to create single-sample glfs. this call is parallelized by calling each region of 5 million base pairs separately. the glfmultiples tool combines all of the sample glfs for one region into a single vcf. the regions are combined into per-chromsome multi-sample vcfs, and variants are filtered to include only passing […]


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