Costumized QC: Add new features for MergeSample and BAM Contamination - Githubissues

NCI-CGR / IlluminaSequencingAnalysis

All Illumina Sequencing Related project from Xin will be recorded in this repo

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Costumized QC: Add new features for MergeSample and BAM Contamination #35

Open lxwgcool opened 2 years ago

lxwgcool commented 2 years ago

Details:

1: MergeSubject.py

(1) Add global variable for SCRIPTMergeSample and DIRRootBuild
(2) Build Mimic Manifest file for reusing the essential code in 2nd pipeline
(3) Add a function to obtain AnalysisID
(4) Finish a function to submit jobs in biowulf

2: Add new function to check BAM contamination

(1) ContaminationCheck.py: main code to do the data pre-processing and automation
(2) ContaminationCheckSingle.sh: the bash code that be used to run verifyBamID.