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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

 (10)
library_books

Multiplex PCR Targeted Amplicon Sequencing (MTA Seq): Simple, Flexible, and Versatile SNP Genotyping by Highly Multiplexed PCR Amplicon Sequencing

2018
Front Plant Sci
PMCID: 5876661
PMID: 29628929
DOI: 10.3389/fpls.2018.00201

[…] he SAMtools “rmdup” command. Plural mapping data of the same accession were merged using the SAMtools “merge” command. For SNP calling, we used freebayes (v0.9.21-15-g8a06a0b) (Garrison and Marth, ), glfMultiples (v2010-06-16) (The 1000 Genomes Project Consortium, ), SAMtools (v0.1.19) (Li et al., ), HaplotypeCaller in GATK (v3.3-0) (McKenna et al., ), and UnifiedGenotyper in GATK (v3.3-0) (McKenn […]

library_books

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

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

[…] 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 (). Som […]

library_books

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

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

[…] de of 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 between 6,823 […]

library_books

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

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

[…] type 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 Genom […]

call_split

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

2015
BMC Res Notes
PMCID: 4423141
PMID: 25926048
DOI: 10.1186/s13104-015-1130-z
call_split See protocol

[…] file : 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) was applied […]

library_books

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

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

[…] n calling singletons. Nevertheless, G-IBC identified about 3% more singletons than G-PBC and these had significantly higher Ts/Tv, replicating the pattern observed in our analyses using glfSingle and glfMultiples. […]

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