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NCI-CGR / IlluminaSequencingAnalysis

All Illumina Sequencing Related project from Xin will be recorded in this repo
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Customized QC: New tool: CombineReport #43

Open lxwgcool opened 2 years ago

lxwgcool commented 2 years ago

Since one build may contain several different batches, we need to merge the related report after all bathes were finished.

It contains three different types of report, including

lxwgcool commented 2 years ago

Tool name

CombineReport.py

How to use it

python 3 CombineReport.py

Example

1: Coverage Report
python3 ./CombineReport.py 1 /data/COVID_WGS/UpstreamAnalysis/PostPrimaryRun/Data/BAM/Batch/low_input_01_96_keytable/Report/Coverage low_input_01_96_keytable

2: Pre-Calling QC Report
python3 ./CombineReport.py 2 /data/COVID_WGS/UpstreamAnalysis/PostPrimaryRun/Data/BAM/Batch/low_input_01_96_keytable/Report/PreCallingQC/ low_input_01_96_keytable

3: BAM Contamination Report
python3 ./CombineReport.py 3 /data/COVID_WGS/UpstreamAnalysis/PostPrimaryRun/Data/BAM/Batch/low_input_01_96_keytable/Report/BAMContaminationCheck/ low_input_01_96_keytable