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Update reference to Full Pseudomolecules #5

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4 of 10 tasks
nathanhaigh opened this issue Jul 9, 2018 · 0 comments
Open
4 of 10 tasks

Update reference to Full Pseudomolecules #5

nathanhaigh opened this issue Jul 9, 2018 · 0 comments
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@nathanhaigh

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@nathanhaigh
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nathanhaigh commented Jul 9, 2018 •
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The latest JBrowse source (currently only in master branch) apparently supports CSI indexes for BAM and VCF files. If this is true, then we can think about the posibility of upgrading the reference sequence from the "parts" version to full-length pseudo molecules. However, there are downstream processing still affected by a lack of CSI index support including operations involving sambamba and GATK which do not support CSI (biod/sambamba#284).

Tasks remaining:

  • Upload full-pseudomolecule NGS data
  • Upload reference-based tracks
  • Add config files for NGS data
  • Add config files for reference-based tracks

Add the following tracks as NCList, assuming this is still needed for search capabilities:

  • Add HC v1.0 genes track as NCList
  • Add LC v1.0 genes track as NCList
  • Add HC v1.1 genes track as NCList
  • Add LC v1.1 genes track as NCList
  • Add DArT Public track as NCList
  • Add DArT ver3 track as NCList
@nathanhaigh nathanhaigh self-assigned this Jan 15, 2019
@nathanhaigh nathanhaigh changed the title Update reference to single-part Update reference to Full Pseudomolecules Jan 22, 2019
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