FreeBayes protocols

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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Documentation


Maintainer


  • person_outline Erik Garrison <>

Publication for FreeBayes

FreeBayes IN pipelines

 (35)
2018
PMCID: 5803254
PMID: 29416032
DOI: 10.1038/s41467-018-03016-2

[…] computed from the .xmap files., genome assemblies were validated with a variant calling based approach. illumina short reads were mapped against each assembly with bwa29 and variations called with freebayes32. 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))33,34. only biallelic […]

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) [11] 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: 5841092
PMID: 29552023
DOI: 10.3389/fpls.2018.00268

[…] around off-target sites were concatenated into a “pseudo-genome” which was used as a mapping reference for the miseq dataset using bwa mem (version: 0.7.15) (li, 2013). variants were called using freebayes (v1.0.2) variant calling program (garrison and marth, 2012) and were visualized in igv (thorvaldsdóttir et al., 2013). truncated alignments were removed and only alignments starting within […]

2018
PMCID: 5933776
PMID: 29723202
DOI: 10.1371/journal.pone.0195860

[…] snps were identified from consensus draft genomes generated through bowtie2 read-mapping to a usa300 reference genome (usa300_fpr3757) [17]. each genomic sequence was compared within a subject using freebayes and snpsift to identify snps common within the set of genomic sequences. forty-two percent of the snps resulted in a predicted amino acid change within a protein coding region (table 4 […]

2018
PMCID: 5940699
PMID: 29739964
DOI: 10.1038/s41598-018-25071-x

[…] to the european nucleotide archive19 under the accession number prjna (deposit in databank under submission)., single nucleotide polymorphisms were called independently for each individual with freebayes24 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 […]

FreeBayes review

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Tristan Dubos

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Desktop
Interesting solution to detect MNPs variation !