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XCAVATOR: accurate detection and genotyping of copy number variants from second and third generation whole-genome sequencing experiments.

ABSTRACT:

Background

We developed a novel software package, XCAVATOR, for the identification of genomic regions involved in copy number variants/alterations (CNVs/CNAs) from short and long reads whole-genome sequencing experiments.

Results

By using simulated and real datasets we showed that our tool, based on read count approach, is capable to predict the boundaries and the absolute number of DNA copies CNVs/CNAs with high resolutions. To demonstrate the power of our software we applied it to the analysis Illumina and Pacific Bioscencies data and we compared its performance to other ten state of the art tools.

Conclusion

All the analyses we performed demonstrate that XCAVATOR is capable to detect germline and somatic CNVs/CNAs outperforming all the other tools we compared. XCAVATOR is freely available at http://sourceforge.net/projects/xcavator/ .

SUBMITTER: Magi A

PROVIDER: S-EPMC5609061 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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XCAVATOR: accurate detection and genotyping of copy number variants from second and third generation whole-genome sequencing experiments.

Magi Alberto A Pippucci Tommaso T Sidore Carlo C

BMC genomics 20170921 1

<h4>Background</h4>We developed a novel software package, XCAVATOR, for the identification of genomic regions involved in copy number variants/alterations (CNVs/CNAs) from short and long reads whole-genome sequencing experiments.<h4>Results</h4>By using simulated and real datasets we showed that our tool, based on read count approach, is capable to predict the boundaries and the absolute number of DNA copies CNVs/CNAs with high resolutions. To demonstrate the power of our software we applied it ...[more]

PMID: 28934930

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