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BAYSIC specifications

Information


Unique identifier OMICS_03611
Name BAYSIC
Alternative name BAYeSian Integrated Caller
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl, R
Computer skills Advanced
Stability Stable
Maintained No

Versioning


No version available

Maintainer


This tool is not available anymore.

Publication for BAYeSian Integrated Caller

BAYSIC citations

 (4)
library_books

A review of somatic single nucleotide variant calling algorithms for next generation sequencing data

2018
Comput Struct Biotechnol J
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] s are assembled and re-aligned.Machine learning methods have been very successful in classification, and variant calling is essentially a classification problem. MutationSeq, SomaticSeq, SNooPer, and BAYSIC , , , are representative variant callers that apply machine learning methods. MutationSeq extracts relevant features on each site and trains four classifiers (random forest, Bayesian adaptive […]

library_books

Population Genomic Analysis of a Pitviper Reveals Microevolutionary Forces Underlying Venom Chemistry

2017
Genome Biol Evol
PMCID: 5737360
PMID: 29048530
DOI: 10.1093/gbe/evx199

[…] ing sequences were called using four separate algorithms: GATK, freebayes, platypus, and samtools (; ; ; ). Variants were converted to allelic primitives using GATK, and a consensus set was called by BAYSIC using a 0.80 posterior probability (). Finally, indels, variants with >10% missing data in the ingroup samples, and variants with more than two alleles were filtered out. We then classified var […]

library_books

Genomic Signature of Kin Selection in an Ant with Obligately Sterile Workers

2017
Mol Biol Evol
PMCID: 5455959
PMID: 28419349
DOI: 10.1093/molbev/msx123

[…] tly, variants were called separately using GATK, FreeBayes and Samtools (; ; ). These variant call sets were converted to allelic primitives using GATK, and combined into a high credibility set using BAYSIC (). We subsequently removed indels, any sites with more than two alleles, with more than 10% missing data, and any with a site quality lower than a phred score of 40 to produce the final varian […]

library_books

Reliably Detecting Clinically Important Variants Requires Both Combined Variant Calls and Optimized Filtering Strategies

2015
PLoS One
PMCID: 4658170
PMID: 26600436
DOI: 10.1371/journal.pone.0143199

[…] iant callers. Implementing this approach requires running multiple variant callers in parallel and combining the results to take forward for analysis, an approach already implemented by tools such as BAYSIC []. While combined variant calls is the ideal strategy, it must be acknowledged that computational resources are often limited in which case it is preferable to run BWA paired with GATK due to […]

Citations

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BAYSIC institution(s)
Baylor Health, Baylor Institute for Immunology Research, Dallas, TX, USA; Genformatic, LLC, Austin, TX, USA

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