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This repository was archived by the owner on Mar 2, 2021. It is now read-only.
This repository was archived by the owner on Mar 2, 2021. It is now read-only.

vcfcluster for pacbio SV calls? #89

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@ggstatgen

Hi

I was wondering if I could use svtk vcfcluster to compare SV calls obtained from long read alignments (basically split-reads based calls only). Is this something you've tested before? I was interested in the following description in vcfcluster help message:

Paired-end and split-read callers provide a reasonably precise estimation of an SV breakpoint. This program identifies variant calls that fall within the expected margin of error made by these programs and clusters them together. The cluster distance defaults to 500 bp but it is recommended to use the maximum individual clustering distance across the libraries being analyzed. (Generally median + 7 * MAD) 

I was wondering if the above was based on your own findings or if perhaps there is a publication source for the 'median + 7*MAD' statement. Thanks!

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