AccuCalc: A Python Package for Accuracy Calculation in GWAS
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F23%3A73622300" target="_blank" >RIV/61989592:15310/23:73622300 - isvavai.cz</a>
Result on the web
<a href="https://www.mdpi.com/2073-4425/14/1/123" target="_blank" >https://www.mdpi.com/2073-4425/14/1/123</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.3390/genes14010123" target="_blank" >10.3390/genes14010123</a>
Alternative languages
Result language
angličtina
Original language name
AccuCalc: A Python Package for Accuracy Calculation in GWAS
Original language description
The genome-wide association study (GWAS) is a popular genomic approach that identifies genomic regions associated with a phenotype and, thus, aims to discover causative mutations (CM) in the genes underlying the phenotype. However, GWAS discoveries are limited by many factors and typically identify associated genomic regions without the further ability to compare the viability of candidate genes and actual CMs. Therefore, the current methodology is limited to CM identification. In our recent work, we presented a novel approach to an empowered "GWAS to Genes" strategy that we named Synthetic phenotype to causative mutation (SP2CM). We established this strategy to identify CMs in soybean genes and developed a web-based tool for accuracy calculation (AccuTool) for a reference panel of soybean accessions. Here, we describe our further development of the tool that extends its utilization for other species and named it AccuCalc. We enhanced the tool for the analysis of datasets with a low-frequency distribution of a rare phenotype by automated formatting of a synthetic phenotype and added another accuracy-based GWAS evaluation criterion to the accuracy calculation. We designed AccuCalc as a Python package for GWAS data analysis for any user-defined species-independent variant calling format (vcf) or HapMap format (hmp) as input data. AccuCalc saves analysis outputs in user-friendly tab-delimited formats and also offers visualization of the GWAS results as Manhattan plots accentuated by accuracy. Under the hood of Python, AccuCalc is publicly available and, thus, can be used conveniently for the SP2CM strategy utilization for every species.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10608 - Biochemistry and molecular biology
Result continuities
Project
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Continuities
S - Specificky vyzkum na vysokych skolach
Others
Publication year
2023
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Genes
ISSN
2073-4425
e-ISSN
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Volume of the periodical
14
Issue of the periodical within the volume
1
Country of publishing house
CH - SWITZERLAND
Number of pages
13
Pages from-to
"123-1"-"123-13"
UT code for WoS article
000916901900001
EID of the result in the Scopus database
2-s2.0-85146758298