Abstract
With the developments in high-throughput sequencing (HTS) technologies, researchers have gained a powerful tool to identify structural variants (SVs) in genomes with substantially less cost than before. SVs can be broadly classified into two main categories: balanced rearrangements and copy number variations (CNVs). Many algorithms have been developed to characterize CNVs using HTS data, with focus on different types and size range of variants using different read signatures. Read depth (RD) based tools are more common in characterizing large (>10 kb) CNVs since RD strategy does not rely on the fragment size and read length, which are limiting factors in read pair and split read analysis. Here we provide a guideline for a user friendly tool for detecting large segmental duplications and deletions that can also predict integer copy numbers for duplicated genes.
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Abbreviations
- CNV:
-
Copy number variation
- mrCaNaVaR:
-
Micro read Copy Number Variant Regions
- mrFAST:
-
Micro read Fast Alignment Search Tool
- mrsFAST:
-
Micro read substitution only Fast Alignment Search Tool
- RD:
-
Read depth
- TRF:
-
Tandem repeat finder
- WGS:
-
Whole genome sequencing
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Kahveci, F., Alkan, C. (2018). Whole-Genome Shotgun Sequence CNV Detection Using Read Depth. In: Bickhart, D. (eds) Copy Number Variants. Methods in Molecular Biology, vol 1833. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8666-8_4
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DOI: https://doi.org/10.1007/978-1-4939-8666-8_4
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