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LoFreq specifications

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Unique identifier OMICS_00063
Name LoFreq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for LoFreq

LoFreq citations

 (53)
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Somatic activating mutations in MAP2K1 cause melorheostosis

2018
PMCID: 5895796
PMID: 29643386
DOI: 10.1038/s41467-018-03720-z

[…] hotspot regions in map2k1 (exons 2, 3, 6, 7, 11), as well as the ras codon 12, 13 and 61 hotspot mutations. the amplicon libraries were sequenced on illumina miseq and variants were called with lofreq 2.1.2., to validate and quantitate the allele frequency of somatic mutations in other tissues and cells cultured ex vivo, we utilized ddpcr (fig. ). the approach determines the abundance […]

library_books

Variant ribosomal RNA alleles are conserved and exhibit tissue specific expression

2018
PMCID: 5829973
PMID: 29503865
DOI: 10.1126/sciadv.aao0665

[…] 8 nt at each read end were reduced to quality score zero (q0) to preclude read termini from analysis and thus the possibility of misalignment contributing to variant calls (fig. s1h). we then used lofreq (), a base quality–aware algorithm designed for conservative detection of rare sequence variants that implements a strand bias test with bonferroni correction, to call statistically […]

library_books

A review of somatic single nucleotide variant calling algorithms for next generation sequencing data

2018
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] variant callers abandon the diploidy assumption and model joint allele frequencies (ft,fn) instead of joint genotypes (gt,gn). the allele frequency analysis approach is taken by strelka, mutect, lofreq, ebcall, deepsnv, lolopicker, and muse , , , , , , . strelka's core algorithm consists of two steps. first, the posterior probabilities of vafs in tumor and normal, noted as p(ft,fn|dt,dn), […]

library_books

Disentangling the Causes for Faster X Evolution in Aphids

2018
PMCID: 5798017
PMID: 29360959
DOI: 10.1093/gbe/evy015

[…] for a. svalbardicum and a. pisum cdss. we restricted the analysis to regions of reliable alignments, as given by the gblocks txts outputs. in these regions, we called snps on the bam files with lofreq (), which offers a good compromise between speed, sensitivity, and accuracy in pools of multiple individuals (). we used samtools mpileup () to assess depth of coverage at all positions […]

library_books

Applying Precision Medicine to Ovarian Cancer

2018
PMCID: 5839702
PMID: 29324546
DOI: 10.1097/IGC.0000000000001190

[…] sequencing (ngs) was performed using an illumina miseq with v2 chemistry. average coverage depth was greater than 6500 times. somatic variant calling was performed using gatk best practices and lofreq to identify variants with a predetermined allele frequency threshold of 1.0%. the average performance metrics for each sample was 96% on target and 99% coverage uniformity as defined by 20% […]

library_books

Selection for long and short sleep duration in Drosophila melanogaster reveals the complex genetic network underlying natural variation in sleep

2017
PMCID: 5730107
PMID: 29240764
DOI: 10.1371/journal.pgen.1007098

[…] thus, the number of polymorphisms segregating within the population was known. 2,222,264 polymorphisms were expected to segregate among the 10 dgrp lines that we used [, ]. in addition, we used lofreq [] to identify additional potential rare or de novo polymorphisms that might be present in our selected populations; lofreq detected an additional 258,268 potential polymorphisms (materials […]


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LoFreq institution(s)
Genome Institute of Singaporet, Genome, Singapore, Singapore; Hoffmann-La Roche,Nutley, NJ, USA

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