Question: gnomAD Structural Variants pipeline usage
1
gravatar for cocchi.e89
3 months ago by
cocchi.e8990
cocchi.e8990 wrote:

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!

ADD COMMENTlink modified 3 months ago • written 3 months ago by cocchi.e8990
2
gravatar for cocchi.e89
3 months ago by
cocchi.e8990
cocchi.e8990 wrote:

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

ADD COMMENTlink written 3 months ago by cocchi.e8990
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