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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


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

PLoS One
PMCID: 5933776
PMID: 29723202
DOI: 10.1371/journal.pone.0195860
call_split See protocol

[…] lasmids (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 (MQM […]


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

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

[…] l 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 and trimm […]


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

Genome Announc
PMCID: 5920189
PMID: 29700146
DOI: 10.1128/genomeA.00294-18
call_split See protocol

[…] apped 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, the […]


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

PLoS One
PMCID: 5918994
PMID: 29694377
DOI: 10.1371/journal.pone.0196058
call_split See protocol

[…] eSeq 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 fr […]


A New Single Nucleotide Polymorphism Database for Rainbow Trout Generated Through Whole Genome Resequencing

Front Genet
PMCID: 5928233
PMID: 29740479
DOI: 10.3389/fgene.2018.00147

[…] ntified.Maximum depth filter (DP): We removed the sites that were covered by excess number of reads as these sites are very likely to be located within a repeat or a multi-duplicated region. Although FreeBayes and SAMtools mpileup report the read depth in slightly different manner due to algorithm differences, we chose the same maximum depth value of 1,500, corresponding to a coverage of 24.6 read […]


EAGLE: Explicit Alternative Genome Likelihood Evaluator

BMC Med Genomics
PMCID: 5918433
PMID: 29697369
DOI: 10.1186/s12920-018-0342-1

[…] from GATK ‘best practices’ [] (see Additional file  for details). We used the resulting BAM format alignment data to call variants with: GATK HaplotypeCaller (3.3.0) [, ], SAMtools mpileup (1.3) [], FreeBayes (1.0.2) [], and Platypus (0.8.1) []. Each callset was normalized using vt normalize [] and the vcfallelicprimitives module in vcflib ( to deconstruct complex va […]


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Anonymous user #27497's avatar image

Anonymous user #27497

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Interesting solution to detect MNPs variation !