BCFtools/csq: haplotype-aware variant consequences | Zendy

Petr Danecek | Zendy; Shane McCarthy | Zendy

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BCFtools/csq: haplotype-aware variant consequences

Author(s) -

Petr Danecek,

Shane McCarthy

Publication year - 2017

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btx100

Subject(s) - indel , haplotype , indel mutation , computer science , 1000 genomes project , data mining , prioritization , categorization , computational biology , sanger sequencing , genome , genetics , biology , artificial intelligence , single nucleotide polymorphism , mutation , gene , management science , genotype , economics

Prediction of functional variant consequences is an important part of sequencing pipelines, allowing the categorization and prioritization of genetic variants for follow up analysis. However, current predictors analyze variants as isolated events, which can lead to incorrect predictions when adjacent variants alter the same codon, or when a frame-shifting indel is followed by a frame-restoring indel. Exploiting known haplotype information when making consequence predictions can resolve these issues.

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