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Implement command to merge SV calling VCFs into single VCF/TSV #46

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holtgrewe opened this issue Apr 17, 2023 · 0 comments · Fixed by #52
Closed
11 tasks done

Implement command to merge SV calling VCFs into single VCF/TSV #46

holtgrewe opened this issue Apr 17, 2023 · 0 comments · Fixed by #52

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@holtgrewe
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holtgrewe commented Apr 17, 2023 •
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This would be equivalent to varfish-annotator annotate-svs.

We should implement support for the following tools:

  • Delly 2
  • Dragen CNV
  • Dragen SV
  • GATK gCNV
  • Manta
  • Melt
  • PopDel

Parts

  • guess caller and version
  • convert into internal representation
  • parse breakend syntax
  • write out as TSV
  • write out as VCF
  • overall clustering
    • read in all VCFs and write out per contig as JSONL
    • read in contig-wise
    • cluster, and
    • write to final format
  • annotate with read depth and average mapping quality #51
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feat: annotation of structural variants (#46) varfish-org/mehari
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