Variant caller plug in v3

Manufactured by Thermo Fisher Scientific

The Variant Caller plug-in v3.6 is a software tool designed to identify genetic variations within DNA sequences. It is intended for use with Next-Generation Sequencing (NGS) data analysis workflows.

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Lab products found in correlation

Torrent suite software v3, by Thermo Fisher Scientific (2 mentions)

2 protocols using variant caller plug in v3

Comprehensive Somatic Mutation Analysis

Cited 1 time

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The raw data were analyzed using the torrent suite software v3.6.2 (Life technologies). The coverage analysis was performed using the coverage analysis plug-in v3.6. Cases for which the number of mapped reads was <100000 and/or the average base coverage was <500x were considered as non informative. Mutations were detected using the Variant Caller plug-in v3.6 with low stringency settings (Life Technologies). In the variant list obtained, each mutation was verified in the Integrative genome viewer (IGV) from the Broad Institute (http://www.broadinstitute.org/igv/) [19 (link)]. Only mutations reported in the COSMIC (Sanger Institute Catalogue of Somatic Mutations in Cancer) database (http://www.sanger.ac.uk/cosmic) were taken into account and silent or intronic mutations were not reported.

D’Haene N., Le Mercier M., De Nève N., Blanchard O., Delaunoy M., El Housni H., Dessars B., Heimann P., Remmelink M., Demetter P., Tejpar S, & Salmon I. (2015). Clinical Validation of Targeted Next Generation Sequencing for Colon and Lung Cancers. PLoS ONE, 10(9), e0138245.

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Comprehensive Genomic Variant Analysis Protocol

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The raw data were analyzed using the torrent suite software v3.6.2 (Life technologies). The coverage analysis was performed using the coverage analysis plug-in v3.6. Cases for which the number of mapped reads was <100000 and/or the average base coverage was <500x were considered as non-informative. Mutations were detected using the Variant Caller plug-in v3.6 with low stringency settings (Life Technologies). In the variant list obtained, each mutation was verified in the Integrative genome viewer (IGV) from the Broad Institute (http://www.broadinstitute.org/igv/). Only mutations reported in the COSMIC (Sanger Institute Catalogue of Somatic Mutations in Cancer) database (http://www.sanger.ac.uk/cosmic) were taken into account and silent or intronic mutations were not reported. Locis were further analyzed for functional prediction of amino acid changes using two different prediction algorithms (Provean and SIFT) [17 (link), 18 (link)].

Lim S.M., Kim H.R., Cho E.K., Min Y.J., Ahn J.S., Ahn M.J., Park K., Cho B.C., Lee J.H., Jeong H.C., Kim E.K, & Kim J.H. (2016). Targeted sequencing identifies genetic alterations that confer primary resistance to EGFR tyrosine kinase inhibitor (Korean Lung Cancer Consortium). Oncotarget, 7(24), 36311-36320.

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