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glfMultiples specifications


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


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

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 (). […]


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

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 […]


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

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 […]


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

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) […]


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

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 (, which also generated variant calls for nhlbi go exome sequencing project (esp) and contributed to 1000 genomes project analyses [,,]., […]


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

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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