ctDNA

Pipelines for analyzing ctDNA targeted sequencing data

This has all the experimental and intermediate pipeline and other scripts.

The two main pipelines you need to look at are:

Name		Name	Last commit message	Last commit date
README.md		README.md
SVpipeline.scala		SVpipeline.scala
Simulation.R		Simulation.R
ctDNAlign.scala		ctDNAlign.scala
ctdnaAlignment.scala		ctdnaAlignment.scala
ctdnaAlignment2_2.scala		ctdnaAlignment2_2.scala
ctdnaAlignment4_5.scala		ctdnaAlignment4_5.scala
ctdnaAlignment6.scala		ctdnaAlignment6.scala
ctdnaAlignmentNovaseq.scala		ctdnaAlignmentNovaseq.scala
ctdnaAlignment_smallspace.scala		ctdnaAlignment_smallspace.scala
ctdnaVariants.scala		ctdnaVariants.scala
ctdnaVariantsCorrected.scala		ctdnaVariantsCorrected.scala
forcedCallingPipeline.scala		forcedCallingPipeline.scala
fragmentAnalysis.R		fragmentAnalysis.R
mutectDoubleCalling.scala		mutectDoubleCalling.scala
mutectDoubleCalling6.scala		mutectDoubleCalling6.scala
mutectDoubleCallingAll.scala		mutectDoubleCallingAll.scala
mutectSingleTumor.scala		mutectSingleTumor.scala
newMutect.scala		newMutect.scala
newMutect2_2.scala		newMutect2_2.scala
newMutect2_2v2.scala		newMutect2_2v2.scala
newMutect_nova.scala		newMutect_nova.scala
newMutect_novaseq.scala		newMutect_novaseq.scala
plotVars.R		plotVars.R
qcPlot.R		qcPlot.R
score_dev.R		score_dev.R
test_params.R		test_params.R

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