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nanoporetech / pipeline-structural-variation

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
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cuteSV nanopore parameters. #21

Open humbleflowers opened 3 years ago

humbleflowers commented 3 years ago

Any reason why cuteSV report parameters for SV calling are not used? cuteSV recommends following parameters according to their gitub page.

For ONT data: --max_cluster_bias_INS 100 --diff_ratio_merging_INS 0.3 --max_cluster_bias_DEL 100 --diff_ratio_merging_DEL 0.3

Thank you.

biorococo commented 3 years ago

Hi @humbleflowers,

The recommended/default parameters have changed in different versions of cuteSV, in internal evaluations we've observed slightly better results by using default parameters, so we stick to them for now. Let me know if you have any other doubt about this.

Thank you very much