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Short description:
Please summarise the application in a few sentences. Avoid links here. Bayesian genetic variant detector (SNPs, indels, MNPs)
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
Genomics
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
Boston College
== Description == <!-- Describe the application in the space below --> FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), and MNPs (multi-nucleotide polymorphisms) smaller than the length of a short-read sequencing alignment. It uses short-read alignments (BAM files with Phred+33 encoded quality scores) for any number of individuals from a population and a reference genome to determine the most-likely combination of genotypes for the population at each position in a reference genome (FASTA). It reports positions which it finds to be more likely polymorphic than monomorphic in a standard variant interchange format (VCF). Manual <i>seems</i> to indicate that Freebayes will work with both indexed (barcoded, or separately run samples so that individual is known for each read) or non-indexed pooled reads. == Usage == In its simplest form (finding SNPs versus a reference) Freebayes can be run by just typing : ./freebayes --fasta-reference input.fa aligned.bam. <!-- -->
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