Publication for ONCOCNV
ONCOCNV in publications(4)
[…] number of pcr amplicons, sequence variation, or pcr enrichment efficiency. for cnv detection in our pcr-enriched amplicon sequencing data of the 20 genes, we used two algorithms, quandico  and oncocnv , specifically developed for cnv analysis of amplicon sequencing data. the cnvs detected with these algorithms were then verified experimentally using the multiplex ligation-dependent probe […]
[…] settings were kept at default values and all computations were done using r/bioconductor., the read counts from aligned and sorted bam files of the ion torrent sequencing were processed using oncocnv with default parameter settings to correct for library size, gc content and amplicon length. the pool of normal samples was used as baseline control to capture the technology specific bias […]
[…] somatic mutations. the limit of detection (lod) and the limit of quantification (loq) were at 1% of maf, as set by the manufacturer. copy number variation (cnv) analysis was performed using the oncocnv package ., blood samples were obtained postoperatively and before the first-line treatment. plasma was extracted from edta-anticoagulated blood samples by centrifuging once at 2000 g (10 […]
[…] involved in the preparation of amplicon libraries result in high depth of coverage at the expense of coverage homogeneity., the first method designed for the investigation of cnv from ams data is oncocnv. duplicate sequences are not removed, while rc is performed assigning “each read to only one amplicon region, the one with which the read alignment has the maximum overlap” (boeva et al., )., […]
This software is very precise (specificity, sensitivity). I'm now using it in diagnostics, on small and large panels of genes.
Missing an annotation of variants