gnomAD Structural Variants pipeline usage
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17 months ago
cocchi.e89 ▴ 170

I am trying to use the recently published gnomad-SV calling pipeline for structural variant calling. They released all code in github and it basically works through .wdl scripts that can be deployed on Terra Firecloud and each of this script looks like calling a docker image that operates the task.

It is pretty difficult to get what the input files are, format, the order of the scripts etc. and also looking at github issues it looks like the whole thing is pretty confusing.

I am wondering if anybody here tried to use this incredible pipeline and managed to get it run somehow.

Thank you very much for any help in advance!

gnomad sv talkowski-lab pipeline • 572 views
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Entering edit mode
17 months ago
cocchi.e89 ▴ 170

Looks like they published an updated and commented repo here: https://github.com/broadinstitute/gatk-sv

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