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Wrapper and analysis scripts for RNA variant calling pipeline

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BrooksLabUCSC/RNA-VaCay

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.gitignore

.gitignore

 
 

BAM_download2.py

BAM_download2.py

 
 

README.md

README.md

 
 

compareWhitelist.R

compareWhitelist.R

 
 

execute-varDict.sh

execute-varDict.sh

 
 

histogramBreakdown.R

histogramBreakdown.R

 
 

makeCompiled.R

makeCompiled.R

 
 

mutect2.sh

mutect2.sh

 
 

normal-vardict.sh

normal-vardict.sh

 
 

platypus.sh

platypus.sh

 
 

post-process-wrap.sh

post-process-wrap.sh

 
 

process-vcf.R

process-vcf.R

 
 

varDict.sh

varDict.sh

 
 

vardict2vcf.py

vardict2vcf.py

 
 

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#RNA-VaCay

Wrapper and analysis scripts for RNA variant calling pipeline. Customized for Mutect2, VarDict, and Platypus. Wrapper scripts written in Bash and analysis scripts written in R.

Must modify paths at top of each script to customize to your directories.

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Wrapper and analysis scripts for RNA variant calling pipeline

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