Annotate long read svs - Githubissues

populationgenomics / production-pipelines

Genomics workflows for CPG using Hail Batch

MIT License

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Closed MattWellie closed 1 week ago

MattWellie commented 1 week ago

Sorry for the delay, this has been half done for a few weeks

Proposed extension to the long-read pipeline:

query metamist for the SV VCFs
re-process the contents by adding the symbolic allele & INFO content required for SVAnnotate
naive merge of all single-sample VCFs into one fat VCF
annotate that VCF