ClinSV suitable for nanopore data?

[mantonglaw]

Hi! I have some data, 30 × WGS，from nanopore sequcing，could I use ClinSV to call CNV?

[MinocheAE]

Hi,

In the SV calling step ClinSV uses Lumpy and CNVnator. For Nanopore data it is better to use a tool such as Sniffles: https://github.com/fritzsedlazeck/Sniffles https://github.com/fritzsedlazeck/Sniffles

However, ClinSV's SV genome browser tracks will be helpful, when visualising candidate variants in a genome browser like IGV.

You could download them from here. See folder the tracks in

Build 38: https://nci.space/_projects/clinsv_b38/refdata-b38_v1.0.tar

or

Build 37: https://www.nci.space/clinsv/refdata-b37_v0.9.tar https://www.nci.space/clinsv/refdata-b37_v0.9.tar

For details on the annotation tracks, please see Figure 1 in the attached document.

Best regards Andre

On 9. Jan 2022, at 15:12, mantonglaw @.***> wrote:

Hi! I have some data, 30 × WGS，from nanopore sequcing，could I use ClinSV to call CNV?

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[MinocheAE]

Figure 1 Default genome browser tracks for manual validation This region and tracks are display if the IGV session is loaded correctly. It shows a commonly deleted repeat sequence.

1) Depth of coverage of control sample NA12878 2) Depth of coverage of input sample 3) Depth of coverage of sequence read bases with a Phred scaled mapping quality >=20 4) Average mapping quality of aligned reads for current sample 5) Coverage standard deviation in 1kb windows of 500 healthy individuals (MGRB cohort) 6) Regions of segmental duplication as determined by Bailey JA et al. 2002 (Seg-Dup, none in this region) 7) Annotated ClinSV calls from Lumpy and CNVnator 8) Discordant pairs of input sample, followed by discordant pairs of control sample NA12878 (scroll down) 9) Split reads of input sample, followed by split reads of control sample NA12878 10) ClinSV variants from 500 healthy control samples (MGRB cohort) called in batches of 15 samples 11) Structural variants deposited in Database of Genomic Variants (DGV); feature name indicates the population allele frequency, study sample size, author and DGV ID. 12) RefSeq genes 13) ENSEMBL genes (used for annotation)

[mantonglaw]

Thanks for your thorough answer! I will try it.