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revamp somatic sv calling & purity/ploidy estimation #573

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ericblanc20 opened this issue Dec 10, 2024 · 0 comments · May be fixed by #582
Open

revamp somatic sv calling & purity/ploidy estimation #573

ericblanc20 opened this issue Dec 10, 2024 · 0 comments · May be fixed by #582

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@ericblanc20
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Is your feature request related to a problem? Please describe.
Somatic SV calling (for WGS data) & purity/ploidy estimation have been neglected, it's time to give them some attention

Describe the solution you'd like

  • Test current implementation of somatic SV calling with most recent manta version, add options to ignore unplaced, unlocalized, decoys, HLA, ... contigs, as well as optionally include user-defined configuration file.
  • Test current ASCAT implementation for WGS, and compare it with manual runs. The wrappers need to be updated.
@tedil tedil linked a pull request Dec 13, 2024 that will close this issue
feat: revamp somatic sv calling purityploidy estimation #582
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feat: revamp somatic sv calling purityploidy estimation bihealth/snappy-pipeline
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@ericblanc20