FermiKit: Assembly-based variant calling for Illumina resequencing data

Bioinformatics

Volumn 31, Issue 22, 2015, Pages 3694-3696

  Li, Heng ^a  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BASE PAIRING; DNA SEQUENCE; GENE DELETION; GENETICS; HUMAN; HUMAN GENOME; INDEL MUTATION; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; BASE PAIRING; GENOME, HUMAN; HUMANS; INDEL MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION;

EID: 84947756393     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv440     Document Type: Article

References (13)

1. Faust,G.G. and Hall,I.M. (2014) Samblaster: fast duplicate marking and structural variant read extraction. Bioinformatics, 30, 2503-2505.
2. Garrison,E. and Marth,G. (2012) Haplotype-based variant detection from short-read sequencing. arXiv:1207.3907.
3. Layer,R.M. et al. (2014) LUMPY: a probabilistic framework for structural variant discovery. Genome Biol., 15, R84.
4. Li,H. (2012) Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics, 28, 1838-1844.
5. Li,H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997.
6. Li,H. (2014a) Fast construction of FM-index for long sequence reads. Bioinformatics, 30, 3274-3275.
7. Li,H. (2014b) Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics, 30, 2843-2851.
8. Li,H. (2015) BFC: correcting illumina sequencing errors. arXiv:1502.03744.
9. Mills,R.E. et al. (2011) Mapping copy number variation by population-scale genome sequencing. Nature, 470, 59-65.
10. Raczy,C. et al. (2013) Isaac: ultra-fast whole-genome secondary analysis on illumina sequencing platforms. Bioinformatics, 29, 2041-2043.
11. Rausch,T. et al. (2012) DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics, 28, i333-i339.
12. Trappe,K. et al. (2014) Gustaf: Detecting and correctly classifying svs in the ngs twilight zone. Bioinformatics, 30, 3484-3490.
13. Zook,J.M. et al. (2014) Integrating human sequence data sets provides a resource of benchmark snp and indel genotype calls. Nat. Biotechnol., 32, 246-251.