Matches in SemOpenAlex for { <https://semopenalex.org/work/W2169744057> ?p ?o ?g. }
- W2169744057 endingPage "1313" @default.
- W2169744057 startingPage "1307" @default.
- W2169744057 abstract "Abstract Motivation: In light of the increasing adoption of targeted resequencing (TR) as a cost-effective strategy to identify disease-causing variants, a robust method for copy number variation (CNV) analysis is needed to maximize the value of this promising technology. Results: We present a method for CNV detection for TR data, including whole-exome capture data. Our method calls copy number gains and losses for each target region based on normalized depth of coverage. Our key strategies include the use of base-level log-ratios to remove GC-content bias, correction for an imbalanced library size effect on log-ratios, and the estimation of log-ratio variations via binning and interpolation. Our methods are made available via CONTRA (COpy Number Targeted Resequencing Analysis), a software package that takes standard alignment formats (BAM/SAM) and outputs in variant call format (VCF4.0), for easy integration with other next-generation sequencing analysis packages. We assessed our methods using samples from seven different target enrichment assays, and evaluated our results using simulated data and real germline data with known CNV genotypes. Availability and implementation: Source code and sample data are freely available under GNU license (GPLv3) at http://contra-cnv.sourceforge.net/ Contact: Jason.Li@petermac.org Supplementary information: Supplementary data are available at Bioinformatics online." @default.
- W2169744057 created "2016-06-24" @default.
- W2169744057 creator A5018655863 @default.
- W2169744057 creator A5032942789 @default.
- W2169744057 creator A5037117618 @default.
- W2169744057 creator A5045165367 @default.
- W2169744057 creator A5060205491 @default.
- W2169744057 creator A5065036346 @default.
- W2169744057 creator A5067418792 @default.
- W2169744057 creator A5077384369 @default.
- W2169744057 creator A5080235829 @default.
- W2169744057 creator A5082677312 @default.
- W2169744057 date "2012-04-02" @default.
- W2169744057 modified "2023-10-18" @default.
- W2169744057 title "CONTRA: copy number analysis for targeted resequencing" @default.
- W2169744057 cites W1973878786 @default.
- W2169744057 cites W1996361222 @default.
- W2169744057 cites W2046601740 @default.
- W2169744057 cites W2090144921 @default.
- W2169744057 cites W2092203068 @default.
- W2169744057 cites W2097331151 @default.
- W2169744057 cites W2101342813 @default.
- W2169744057 cites W2102619694 @default.
- W2169744057 cites W2103441770 @default.
- W2169744057 cites W2106542343 @default.
- W2169744057 cites W2108698786 @default.
- W2169744057 cites W2114104545 @default.
- W2169744057 cites W2116138166 @default.
- W2169744057 cites W2119180969 @default.
- W2169744057 cites W2120950849 @default.
- W2169744057 cites W2144759168 @default.
- W2169744057 cites W2150506261 @default.
- W2169744057 cites W2160444236 @default.
- W2169744057 doi "https://doi.org/10.1093/bioinformatics/bts146" @default.
- W2169744057 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/3348560" @default.
- W2169744057 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/22474122" @default.
- W2169744057 hasPublicationYear "2012" @default.
- W2169744057 type Work @default.
- W2169744057 sameAs 2169744057 @default.
- W2169744057 citedByCount "290" @default.
- W2169744057 countsByYear W21697440572012 @default.
- W2169744057 countsByYear W21697440572013 @default.
- W2169744057 countsByYear W21697440572014 @default.
- W2169744057 countsByYear W21697440572015 @default.
- W2169744057 countsByYear W21697440572016 @default.
- W2169744057 countsByYear W21697440572017 @default.
- W2169744057 countsByYear W21697440572018 @default.
- W2169744057 countsByYear W21697440572019 @default.
- W2169744057 countsByYear W21697440572020 @default.
- W2169744057 countsByYear W21697440572021 @default.
- W2169744057 countsByYear W21697440572022 @default.
- W2169744057 countsByYear W21697440572023 @default.
- W2169744057 crossrefType "journal-article" @default.
- W2169744057 hasAuthorship W2169744057A5018655863 @default.
- W2169744057 hasAuthorship W2169744057A5032942789 @default.
- W2169744057 hasAuthorship W2169744057A5037117618 @default.
- W2169744057 hasAuthorship W2169744057A5045165367 @default.
- W2169744057 hasAuthorship W2169744057A5060205491 @default.
- W2169744057 hasAuthorship W2169744057A5065036346 @default.
- W2169744057 hasAuthorship W2169744057A5067418792 @default.
- W2169744057 hasAuthorship W2169744057A5077384369 @default.
- W2169744057 hasAuthorship W2169744057A5080235829 @default.
- W2169744057 hasAuthorship W2169744057A5082677312 @default.
- W2169744057 hasBestOaLocation W21697440571 @default.
- W2169744057 hasConcept C104317684 @default.
- W2169744057 hasConcept C111919701 @default.
- W2169744057 hasConcept C120821319 @default.
- W2169744057 hasConcept C124101348 @default.
- W2169744057 hasConcept C141231307 @default.
- W2169744057 hasConcept C174183944 @default.
- W2169744057 hasConcept C2777904410 @default.
- W2169744057 hasConcept C41008148 @default.
- W2169744057 hasConcept C54355233 @default.
- W2169744057 hasConcept C86803240 @default.
- W2169744057 hasConceptScore W2169744057C104317684 @default.
- W2169744057 hasConceptScore W2169744057C111919701 @default.
- W2169744057 hasConceptScore W2169744057C120821319 @default.
- W2169744057 hasConceptScore W2169744057C124101348 @default.
- W2169744057 hasConceptScore W2169744057C141231307 @default.
- W2169744057 hasConceptScore W2169744057C174183944 @default.
- W2169744057 hasConceptScore W2169744057C2777904410 @default.
- W2169744057 hasConceptScore W2169744057C41008148 @default.
- W2169744057 hasConceptScore W2169744057C54355233 @default.
- W2169744057 hasConceptScore W2169744057C86803240 @default.
- W2169744057 hasIssue "10" @default.
- W2169744057 hasLocation W21697440571 @default.
- W2169744057 hasLocation W21697440572 @default.
- W2169744057 hasLocation W21697440573 @default.
- W2169744057 hasLocation W21697440574 @default.
- W2169744057 hasLocation W21697440575 @default.
- W2169744057 hasOpenAccess W2169744057 @default.
- W2169744057 hasPrimaryLocation W21697440571 @default.
- W2169744057 hasRelatedWork W2347219288 @default.
- W2169744057 hasRelatedWork W2347547156 @default.
- W2169744057 hasRelatedWork W2348097614 @default.
- W2169744057 hasRelatedWork W2354822586 @default.
- W2169744057 hasRelatedWork W2356158875 @default.
- W2169744057 hasRelatedWork W2358841807 @default.