SV pipeline for local installation

[cogrho]

Hi!

Is it possible to load structural variants or at least CNV variants from GATK gCNV files to seqr local instance? If not, is it planned to support SV and CNV calls for local installs at some point?

Thanks!

[hanars]

CNV and SV calls are currently not supported in local seqr, but we do have plans to add that support in 2023. The major barrier right now is that the CNV/SV call files we used for our original implementation are a bit "bespoke" and do not conform to any standard/ publicly available calling pipeline. Our hope is to standardize our pipeline this year to be able to either handle standard GATK files and/or provide clear documentation about how to generate the input files seqr requires

[hanars]

We are unfortunately still blocked on having a stable, publicly available calling pipeline for this data. We are hoping to have that finalized in late fall of this year

[anjalijain22]

That sounds good! Thanks for your prompt response!

[anjalijain22]

Hi Hana! Hope you're well :)
Apologies to keep bugging you but I was wondering if there was any update on the CNV/SV pipeline for local installs? We have a ton of positive feedback from our users of the seqr local instance for small variants and there is a growing interest to use seqr for SV/CNV data exploration as well. Thanks in advance for your help!

[hanars]

Hi Anjali, unfortunately not. We will post in the announcements channel once there is any progress on this front! We are glad folks are finding seqr so useful and we are excited to make this functionality available as soon as we can get over the technical and data-normalization hurdles

[anjalijain22]

Thanks for sharing this, we're are looking forward to it!

[gilmorera]

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