| Autor: |
Izaak Coleman, Giacomo Corleone, James Arram, Ho-Cheung Ng, Luca Magnani, Wayne Luk |
| Jazyk: |
angličtina |
| Rok vydání: |
2020 |
| Předmět: |
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| Zdroj: |
BMC Bioinformatics, Vol 21, Iss 1, Pp 1-12 (2020) |
| Druh dokumentu: |
article |
| ISSN: |
1471-2105 |
| DOI: |
10.1186/s12859-020-3367-3 |
| Popis: |
Abstract Background Current popular variant calling pipelines rely on the mapping coordinates of each input read to a reference genome in order to detect variants. Since reads deriving from variant loci that diverge in sequence substantially from the reference are often assigned incorrect mapping coordinates, variant calling pipelines that rely on mapping coordinates can exhibit reduced sensitivity. Results In this work we present GeDi, a suffix array-based somatic single nucleotide variant (SNV) calling algorithm that does not rely on read mapping coordinates to detect SNVs and is therefore capable of reference-free and mapping-free SNV detection. GeDi executes with practical runtime and memory resource requirements, is capable of SNV detection at very low allele frequency ( |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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