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FreeBayes specifications


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




No version available



  • person_outline Erik Garrison <>

Publication for FreeBayes

FreeBayes citations


Whole genome sequencing in the search for genes associated with the control of SIV infection in the Mauritian macaque model

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 […]


Genomic evolution of Staphylococcus aureus isolates colonizing the nares and progressing to bacteremia

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 ( 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 […]


Antibodies to in silico selected GPI anchored Theileria parva proteins neutralize sporozoite infection in vitro

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

[…] short read aligner ( set at default settings. duplicates were marked using picard tools ( 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 […]


Ginkgo biloba’s footprint of dynamic Pleistocene history dates back only 390,000 years ago

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 […]


Whole Genome Sequences of 18 Bovine Alphaherpesvirus 1 Field Isolates from Pennsylvania and Minnesota

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 ( based on phylogenetic analysis, […]


A framework for the estimation of the proportion of true discoveries in single nucleotide variant detection studies for human data

PMCID: 5918994
PMID: 29694377
DOI: 10.1371/journal.pone.0196058

[…] datasets are downloaded in fastq format and aligned with bwa in partek flow. after that, duplicates are removed using filter alignments task and the variant calls are obtained using samtools and freebayes in partek flow. for wes data, the calls are restricted to the corresponding nextera or trueseq target regions., all of the calls are restricted to chromosomes 1–22 and x (na12878 is derived […]

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FreeBayes review

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Tristan Dubos

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Interesting solution to detect MNPs variation !