Integration of ClinSV and additional IGV browser tracks possible?

[boschann]

Would it be possible to integrate the ClinSV framework in our SV analysis pipeline?
https://github.com/KCCG/ClinSV

Would it be possible to provide an IGV genome browser session fileI with additional tracks as shown in Figure 1).
https://github.com/KCCG/ClinSV/blob/master/results_test_data/result_description.docx

[holtgrewe]

Also adding comment by Felix from an email:

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Dear Cubi,

would it be possible classify called SVs into three categories:

1)High quality

2)Pass

3)Low

I like the strategy that was applied in the ClinSV paper: https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-021-00841-x

Are the parameters adoptable to our pipeline?

A) CNV

high confidence: > 100kb, > 10kb + average mapping quality > 55

pass: > 10 kb, <10 kb AND >= 2 split-reads AND/OR discordant read pairs

B) SV

high confidence: >= 10 split-reads AND/OR discordant read pairs count AND at least one of each category

pass: >=6 split-reads AND/OR discordant read pairs AND at least one of each category

The thresholds are of course arbitrary, but we have to set them somewhere.

Best,

Felix