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FreeBayes specifications

Information


Unique identifier OMICS_00059
Name FreeBayes
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Erik Garrison <>

Publication for FreeBayes

FreeBayes in pipelines

 (89)
2018
PMCID: 5802798
PMID: 29410482
DOI: 10.1038/s41598-018-20705-6

[…] markduplicates. read depth and coverage were assessed with samtools ver. 1.2 and bedtools ver. 1.2. consensus fasta sequences for haplogroup prediction and sequence analyses were generated with freebayes ver. 1.0.2–33-gdbb6160 calling the base supported by the 3/5 majority of reads (supplementary table )., to examine data authenticity, we used mapdamage 2.0 to estimate human dna damage […]

2018
PMCID: 5803254
PMID: 29416032
DOI: 10.1038/s41467-018-03016-2

[…] was computed from the .xmap files., genome assemblies were validated with a variant calling based approach. illumina short reads were mapped against each assembly with bwa and variations called with freebayes. genome-wide quality values (q) for snps, insertions, and deletions were calculated as q = −10×log10(total length of variants / total length of sites (dp >3)),. only biallelic variants […]

2018
PMCID: 5811070
PMID: 29390024
DOI: 10.1371/journal.ppat.1006843

[…] described []. for alignment of 75c δ648–659 virus mutant, paired end dna-seq reads were aligned against the reference using bowtie2 [] with default parameters. variants were detected using the freebayes tool [] at depth coverage of at least 500 where the minimum base quality and mapping quality requirements were set to 20 on the phred quality scale., 1.2 x 105 fibroblasts were seeded […]

2018
PMCID: 5820677
PMID: 29568747
DOI: 10.1155/2018/3103986

[…] pipeline was applied to assemble 99 bp sequence reads. the sequence reads were aligned using burrows-wheeler aligner (bwa) to the human reference genome (hg19) [] and variants were submitted using freebayes. an overall quality check of uploaded read data was then performed, including the coverage and average read depth of targeted regions and quality scores. genesis 2.0 […]

2018
PMCID: 5824822
PMID: 29476136
DOI: 10.1038/s41467-018-02826-8

[…] samtools: 1.1 (using htslib 1.1), picard tools: 1.97 (1504), gatk: appistry v2015.1.1–3.4.46–0-ga8e1d99, cnvkit: 0.7.2, pindel: 0.2.5b8, satk: appistry v2015.1.1–1-gea45d62, annovar: v2016feb01, freebayes: 0.9.20, and delly: 0.7.2–. single nucleotide variants and insertions/deletions were visualized and verified using integrated genome viewer. genome-wide copy number analysis based […]


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FreeBayes in publications

 (332)
PMCID: 5940699
PMID: 29739964
DOI: 10.1038/s41598-018-25071-x

[…] to the european nucleotide archive under the accession number prjna (deposit in databank under submission)., single nucleotide polymorphisms were called independently for each individual with freebayes using the following parameters:–standard-filters–no-population-priors -p 2–report-genotype-likelihood-max -c 3. a callability mask was constructed to identify regions of the reference […]

PMCID: 5933776
PMID: 29723202
DOI: 10.1371/journal.pone.0195860

[…] (pusa01, pusa02, and pusa03). duplicates were marked and excluded from further analysis using picard2 removeduplicates tool (http://broadinstitute.github.io/picard). snps were identified with freebayes v1.0.2.29 [] using a list (-l) to compare all genomes from a single subject compared to the reference sequence (usa300_fpr3757) and filtered using snpsift [] for the following qualities […]

PMCID: 5956992
PMID: 29678234
DOI: 10.1016/j.vetimm.2018.03.004

[…] short read aligner (www.sanger.ac.uk/resources/software/smalt) set at default settings. duplicates were marked using picard tools (http://broadinstitute.github.io/picard) set at default parameters. freebayes () was used for calling single nucleotide polymorphisms (parameters: −k −i −x −u −q 20 −min-coverage 6). snps were annotated using snpeff ()., the procedure for sporozoites production […]

PMCID: 5921299
PMID: 29703145
DOI: 10.1186/s12864-018-4673-2

[…] samples’ illumina reads where then mapped to this reference sequence using bwa version 0.7.5a []. after quality filtering and deduplication with samtools version 1.6 [], variants where called using freebayes version 1.1.0-50 [] and consensus sequences extracted as fasta with bcftools version 1.6 []. the resulting sequences where aligned using clustal omega [], the alignment was checked […]

PMCID: 5920189
PMID: 29700146
DOI: 10.1128/genomeA.00294-18

[…] to the national veterinary services laboratory (nvsl) reference/challenge cooper strain of bhv-1.1 (genbank accession number jx898220) using the bwa-mem algorithm (). variants were called using freebayes (). low-quality variants were filtered out, and consensus sequences were obtained using the bcftools consensus tool (http://github.com/samtools/bcftools). based on phylogenetic analysis, […]


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FreeBayes review

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Tristan Dubos

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Desktop
Interesting solution to detect MNPs variation !