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LoFreq specifications

Information


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 in pipelines

 (13)
2018
PMCID: 5829973
PMID: 29503865
DOI: 10.1126/sciadv.aao0665

[…] with gatk, and the quality scores of read termini were manually reduced to q0 to preclude their contribution to variant calling, again as described above (see the “calling rrna variants” section). lofreq, which implements the strand bias test and accounts for quality scores and has been proven to have an extremely low false-positive rate, was then used to call sequence variants. per-sample afs […]

2017
PMCID: 5384157
PMID: 28388925
DOI: 10.1186/s12985-017-0741-5

[…] sequence was then re-called based on bwa-mem mapping of trimmed but un-normalized read data to the genome scaffold and parsing of the mpileup alignment using in-house software. as a final step, lofreq [] was used to estimate variant frequencies in the obtained genomic data. a graphic representation of all major steps included in the sample preparation and analyses is provided in additional […]

2017
PMCID: 5404283
PMID: 28438140
DOI: 10.1186/s12864-017-3714-6

[…] reference sequence until a consensus is generated based on the maximum frequency of nucleotide at a given position []. this process was conducted individually for each of the eleven rov segments. lofreq2 was then used to detect the single nucleotide variants present in the sample []. visualization of the genome coverage graph for the segments of interest and snps identified by lofreq2 […]

2017
PMCID: 5506507
PMID: 28361286
DOI: 10.1007/s00705-017-3342-0

[…] (snvs) and indels, if any, within the inoculum population were identified from the subsampled mapping using two separate programs; namely samtools [] and the low allele frequency variant caller, lofreq []. variants from both programs were compared using bcftools [] and differences inspected manually in the integrative genomics viewer []. a final consensus sequence of the dominant prrsv lv […]

2017
PMCID: 5658298
PMID: 29094026
DOI: 10.4174/astr.2017.93.4.173

[…] realignment, and recalibration, was performed using gatk best practice of broad institute []., at the variant discovery step, the snvs and indels utilized 3 open source callers (unifiedgenotyper [], lofreq [], and snver []) and samsung sds's in-house callers. cnv and translocation were discovered with in-house callers developed by samsung sds. snvs and indels were detected with an ensemble […]


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LoFreq in publications

 (48)
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 […]

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 […]

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), […]

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 […]

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% […]


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

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