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Modify DGV annotations to more general tab format to support complex SVs #307

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zhemingfan opened this issue Feb 9, 2022 · 0 comments
Open
4 tasks

Modify DGV annotations to more general tab format to support complex SVs #307

zhemingfan opened this issue Feb 9, 2022 · 0 comments
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@zhemingfan
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enhancement long read support Support for long read sequence data, e.g. from Oxford Nanopore or PacBio reference files To do with generating the reference input files
Milestone
v3.1.0

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@zhemingfan
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Overview

Currently, the Summary module takes in a tab delimited file (similar to a .bed file) as the input. For future iterations, we want to change it to a MAVIS .tab file format so that more information is included.

  • Change support in summary from tab delimited file to MAVIS file format, rename DGV to "known_sv" as SVs from more databases will be added
  • Add column for support for frequency of which a variant is observed
  • Add unit tests for data that pulls from external and internal Nanpore databases (decide on TSV or VCF file formats to support)
  • Add unique ID support to delineate which dataset a call is from
@zhemingfan zhemingfan added enhancement long read support Support for long read sequence data, e.g. from Oxford Nanopore or PacBio reference files To do with generating the reference input files labels Feb 9, 2022
@zhemingfan zhemingfan added this to the v3.0.0 milestone Feb 9, 2022
@zhemingfan zhemingfan self-assigned this Feb 9, 2022
@creisle creisle changed the title Add Nanopore support in the summary module Modify DGV annotations to more general tab format to support complex SVs Feb 19, 2022
@creisle creisle modified the milestones: v3.0.0, v3.1.0 Feb 22, 2022
@zhemingfan zhemingfan mentioned this issue Apr 26, 2022
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@zhemingfan zhemingfan mentioned this issue Oct 18, 2022
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enhancement long read support Support for long read sequence data, e.g. from Oxford Nanopore or PacBio reference files To do with generating the reference input files
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Milestone
v3.1.0
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@creisle @zhemingfan