Rapid development of next generation sequencing (NGS) technology has substantially improved our ability to detect genomic variations. However, unlike other variations, such as point mutations, insertions, and deletions, which can be identified in high sensitivities and specificities based on NGS reads, most of inversions, especially those shorter than 1 kb, remain difficult to detect. Here we introduce a new framework, SRinversion, which was developed specifically for detection of inversions shorter than 1 kb by splitting and realigning poorly mapped or unmapped reads of the NGS data.
Short inversion detection NGS Structural variations Split reads method
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Lakich D, Kazazian HH Jr, Antonarakis SE et al (1993) Inversions disrupting the factor VIII gene are a common cause of severe haemophilia A. Nat Genet 5(3):236–241CrossRefPubMedGoogle Scholar
Bondeson ML, Dahl N, Malmgren H et al (1995) Inversion of the IDS gene resulting from recombination with IDS-related sequences is a common cause of the Hunter syndrome. Hum Mol Genet 4(4):615–621CrossRefPubMedGoogle Scholar
Gimelli G, Pujana MA, Patricelli MG et al (2003) Genomic inversions of human chromosome 15q11-q13 in mothers of Angelman syndrome patients with class II (BP2/3) deletions. Hum Mol Genet 12(8):849–858CrossRefPubMedGoogle Scholar
Trappe K, Emde AK, Ehrlich HC et al (2014) Gustaf: detecting and correctly classifying SVs in the NGS twilight zone. Bioinformatics 30(24):3484–3490CrossRefPubMedGoogle Scholar
Ye K, Schulz MH, Long Q et al (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25(21):2865–2871CrossRefPubMedPubMedCentralGoogle Scholar
Stankiewicz P, Lupski JR (2010) Structural variation in the human genome and its role in disease. Annu Rev Med 61:437–455CrossRefPubMedGoogle Scholar
Chen R, Lau YL, Zhang Y et al (2016) SRinversion: a tool for detecting short inversions by splitting and re-aligning poorly mapped and unmapped sequencing reads. Bioinformatics 32(23):3559–3565PubMedGoogle Scholar
Cock PJA, Fields CJ, Goto N et al (2009) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 38(6):1767–1771CrossRefPubMedPubMedCentralGoogle Scholar