Name		Name	Last commit message	Last commit date
db		db
zeng2MAFFill		zeng2MAFFill
.gitignore		.gitignore
.hgignore		.hgignore
CHANGELOG.md		CHANGELOG.md
CMDS		CMDS
DMP_rescue.py		DMP_rescue.py
GeneralizedRead.py		GeneralizedRead.py
PAWK.py		PAWK.py
README.md		README.md
TCGA_MAF.py		TCGA_MAF.py
VcfParser.py		VcfParser.py
annotateMAF.py		annotateMAF.py
bPostProcess.sh		bPostProcess.sh
bProcess.sh		bProcess.sh
bgzip		bgzip
deliver.sh		deliver.sh
facetsPost.sh		facetsPost.sh
fillOutMAF_CBE.sh		fillOutMAF_CBE.sh
genomeInfo.sh		genomeInfo.sh
getGermlineMaf.sh		getGermlineMaf.sh
indelOnly.py		indelOnly.py
maf2vcfSimple.sh		maf2vcfSimple.sh
mkTaylorMAF.py		mkTaylorMAF.py
mkTaylorMAFV2.py		mkTaylorMAFV2.py
normalizeInDels.py		normalizeInDels.py
oldMAF2tcgaMAF.py		oldMAF2tcgaMAF.py
pA_FilterA.py		pA_FilterA.py
pA_FilterConsequence.py		pA_FilterConsequence.py
pA_GermlineV2.py		pA_GermlineV2.py
pA_qSomHC.py		pA_qSomHC.py
paths.sh		paths.sh
postProcess.sh		postProcess.sh
sortByRef.pl		sortByRef.pl
tabix		tabix
util.py		util.py
vcf2maf0.py		vcf2maf0.py

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Variant-PostProcess

To use clone version to someplace on LUNA. Then to run

$CLONEDIR/bProcess.sh <PIPELINE_OUTPUT_DIR>

For example:

/home/socci/Code/Bin/PostProcessV1/bProcess.sh /ifs/res/seq/faginj/knaufj/Proj_05873_D/r_002

which should create if successful:

Proj_05873_D___SOMATIC.vep.maf - Somatic MAF file annotated with VEP
Proj_05873_D___FILLOUT.vep.maf - Global FillOut of events in Somatic MAF

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Postprocessing scripts for CBE Variant Pipeline

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