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



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FreeBayes article

FreeBayes citations

PMCID: 5928233

[…] shotgun resequencing for snp discovery in a panel of 11 dh lines and 50 outbred fish from hatchery and natural populations. the snps in our database were called by both the samtools mpileup and freebayes variant identification pipelines and passed through stringent qc filters. the distribution of the snps on chromosomes, the chromosome sequence lengths, the number of snps and the average […]

PMCID: 5944264

[…] were created. bwa version 0.7.5a2 was used to map (aln/sampe) trimmed reads against the reference genome of j. curcas jat r4.5.3 variant discovery and genotyping of samples was performed with freebayes v0.9.94 using specific parameters “–min-base-quality 10 –min-supporting-allele-qsum 10 –read-mismatch-limit 3 -min-coverage 5 –min-alternate-count 4 –report-genotype-likelihood-max […]

PMCID: 5639480

[…] (hasan et al., 2015). to further validate our findings, we developed a sequence-evaluation tool, which we called baysnpper (figure s3a; baysnpper utilized freebayes (fb) (garrison and marth, 2012) to create composite calls from forward and reverse sequence reads and snpeff to make predictions about the indel effect (cingolani et al., 2012). data […]

PMCID: 5436647

[…] [25]. freebayes parameters were set to assume a haploid organism and required a minimum alternate allele fraction of 0.05. variants were filtered for quality and read depth, also using freebayes. at each genomic position (locus) we required at least 100 reads per locus for validity. the amplification and sequencing process can introduce mutations into the resulting data. […]

PMCID: 5445603

[…] sequenced on the illumina miseq platform for a targeted depth of no less than 500 × for any individual amplicon. a custom-built bioinformatics pipeline utilizing gsnap for sequence alignment and freebayes for variant calling was employed for data analysis. all genomic regions were verified to be covered by at least 500 sequencing reads, and identified variants were manually inspected using […]

FreeBayes review

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Tristan Dubos

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Interesting solution to detect MNPs variation !