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ca2905e5

Commit ca2905e5 authored 10 years ago by Peter van 't Hof

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- Added wrapper for Star

- Added a mapping module (not yet used in Gatk)
- Added VariantRecalibrator to Gatk

parent b26d817a

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biopet-framework/src/main/java/nl/lumc/sasc/biopet/core/Config.scala 22 additions, 9 deletions

...ework/src/main/java/nl/lumc/sasc/biopet/core/Config.scala
biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Bwa.scala 39 additions, 8 deletions

...work/src/main/java/nl/lumc/sasc/biopet/wrappers/Bwa.scala
biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala 58 additions, 0 deletions

...ork/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala
flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala 15 additions, 5 deletions

...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala 139 additions, 62 deletions

...c/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
mapping/.gitignore 1 addition, 0 deletions

mapping/.gitignore
mapping/README 0 additions, 0 deletions

mapping/README
mapping/pom.xml 122 additions, 0 deletions

mapping/pom.xml
mapping/run_mapping.sh 8 additions, 0 deletions

mapping/run_mapping.sh
mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala 157 additions, 0 deletions

.../java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
pom.xml 1 addition, 0 deletions

pom.xml

with 562 additions and 84 deletions

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