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Add missing EAGER1 functionality #302

Closed
15 tasks done
jfy133 opened this issue Dec 4, 2019 · 2 comments
Closed
15 tasks done

Add missing EAGER1 functionality #302

jfy133 opened this issue Dec 4, 2019 · 2 comments
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@jfy133
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feature
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V2.1 "Ravensburg"

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jfy133 commented Dec 4, 2019 •
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Is your feature request related to a problem? Please describe.

'EAGER2' should (within reason) reach functional parity with EAGER1.

The options are

  • FastQC
  • Adapter Removal/Merging [Drop Clip&Merge as not maintained and slower]
  • Quality Filtering [Remove as can be done with AdapterRemoval when turn off merging and large overlap]
  • Mapping
  • BAM filtering
  • Complexity Estimation
  • Remove Duplicates
  • Mt2NucRatio
  • PMDTools
  • Contamination Estimation [Replace Schmutzi with ANGSD system]
  • Damage Calculation
  • SNP Calling
  • SNP Filtering [No evidence ever used this - drop for steamlinging]
  • VCF2Genome
  • Report
@jfy133 jfy133 added the feature label Dec 4, 2019
@jfy133 jfy133 added this to the V2.1 "Ulm" milestone Dec 4, 2019
@jfy133 jfy133 self-assigned this Dec 4, 2019
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jfy133 commented Dec 4, 2019

Mt2NucRatio: #304

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jfy133 commented Dec 5, 2019

VCF2Genome: #305

@jfy133 jfy133 closed this as completed Dec 5, 2019
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