LoFreq protocols

LoFreq specifications


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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  • person_outline Niranjan Nagarajan <>

Publication for LoFreq

LoFreq IN pipelines

PMCID: 5757203
PMID: 29379323
DOI: 10.2147/LCTT.S147841

[…] sequences obtained were aligned to human reference genome (grch37/hg19) using bwa program32,33 and processed using picard and gatk toolkits.34,35 the low frequency variants were identified using lofreq program. an in-house method has been developed to filter the low frequency variant to control false positive rate at ultra-high depth sequencing of the samples. we have applied a voting based […]

PMCID: 5890993
PMID: 29630678
DOI: 10.1371/journal.pone.0195272

[…] degradation above a read depth of 5,000x. trimmed fastq files were aligned to hg19 using bwa-mem[24]. for indel calling, base quality scores were recalibrated and indels realigned using gatk[25]. lofreq[11] was then used to create pile-ups of all quality-filtered base calls as each position in the panel for all replicates from spike samples and background control samples. custom perl scripts […]

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

[…] and recalibration, was performed using gatk best practice of broad institute [10]., at the variant discovery step, the snvs and indels utilized 3 open source callers (unifiedgenotyper [11], lofreq [12], and snver [13]) 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 […]

PMCID: 5013668
PMID: 27576846
DOI: 10.1038/ncomms12609

[…] the novoalign3 (http://www.novocraft.com/). after the initial read alignment, indel realignment was performed using abra20 to increase mapping/alignment accuracy21. three mutation callers, mutect17, lofreq22 and pindel23 were used for the detection of single nucleotide variants and indels with the re-aligned binary sequence alignment/map (bam) files24. the resulting mutation calls were annotated […]

PMCID: 5125353
PMID: 27965688
DOI: 10.3389/fpls.2016.01779

[…] the corresponding wild-type control sequence using the same procedure as previously described, except that a maximum edit distance of n = 4 was applied for bwaaln., snp calling was performed using lofreq software (wilm et al., 2012). only snps with a quality above 200 and a frequency above 5% were retained. snps were considered as rb mutations if they are detected in one of the tog7291 […]

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

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