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DSL2: pop-gen #924

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6 of 7 tasks
jfy133 opened this issue Oct 7, 2022 · 0 comments
Open
6 of 7 tasks

DSL2: pop-gen #924

jfy133 opened this issue Oct 7, 2022 · 0 comments
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@TCLamnidis @JoshuaDanielRubin @scarlhoff
Labels
DSL2 enhancement New feature or request
Milestone
3.0 Augsburg

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@jfy133
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jfy133 commented Oct 7, 2022 •
edited by scarlhoff
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  • DEDUP/MARKDUPLICATES
  • MTNUCRATIO
  • NUCLEARCONTAMINATION (HUMAN)
  • SEXDETERRMINE
  • PMDTOOLS
  • BAMUTILS
  • MAPDAMAGE2 (RESCALE)
  • GATKUNIFIEDGENOTYPER
  • GATKHAPLOTYPECALLER
  • PILEUPCALLER
  • FREEBAYES
  • ANGSD

NEW

  • Dedup parallisation (per chromosome)
  • HAPLOGREP
  • HAPLOCART
  • AUTHENTICT
  • Extra genotypers? samtools pileupcaller?
  • Combine SS & DS genotpyes

Tasks
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  1. Dsl2 deduplication #944
    DSL2
  2. DSL2: Add Mtnucratio #958
    pending
    jbv2
  3. DSL2: Adding angsd contamination estimation #976
  4. Dsl2 sex determination #1035
    jbv2
  5. Dsl2 map damage #1045
  6. DSL2: genotyping #1016
  7. Mitochondrial and Ych haplotype callers #917
    DSL2 enhancement
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Assignees

@TCLamnidis TCLamnidis

@JoshuaDanielRubin JoshuaDanielRubin

@scarlhoff scarlhoff

Labels
DSL2 enhancement New feature or request
Projects
No open projects
nf-core Hackathon March 2023
Status: No status
Milestone
3.0 Augsburg
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4 participants
@jfy133 @TCLamnidis @JoshuaDanielRubin @scarlhoff