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ryanlayer / stix

Structural Variant Index
MIT License
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Support for translocations #8

Open amcpherson opened 4 years ago

amcpherson commented 4 years ago

Does STIX support genotyping of translocations? If so could an example be provided in the README? If not, what would be involved to support translocations and would you be willing to provide advice on how to implement, and potentially accept a pull request?

ryanlayer commented 4 years ago

The data is all there, and I have been meaning to add this support for a while. The major limitation right now is decoding the VCF spec for BNDs. In particular, managing all of the strand combinations both internally and as command-line operations. I am tempted to ignore those complexities (strands) for now, so STIX would just look to see if locus A touches locus B. This GREATLY simplify implementation and usage. Thoughts?

On Fri, May 8, 2020 at 11:56 AM Andrew McPherson notifications@github.com wrote:

Does STIX support genotyping of translocations? If so could an example be provided in the README? If not, what would be involved to support translocations and would you be willing to provide advice on how to implement, and potentially accept a pull request?

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