README.md

CNV calling pipeline

This is a pipeline for calling copy number variations from 76 matched tumor-normal whole genome sequencing (WGS) bams from 38 childhood acute lymphoblastic leukemia cases. BAM files have been preprocessed by the data preprocessing pipeline. Check out these GATK best practice documents:

• cnv_somatic_pair_workflow WDL
• (How to part I) Sensitively detect copy ratio alterations and allelic segments
• (How to part II) Sensitively detect copy ratio alterations and allelic segments
• legacy tutorial

GATK somatic CNV calling pipeline:

from 0.0.ExtractIntervalfromPON.sh to 1.9.FuncotateSegments.sh

Best practice workflow. A figure from GITC.

CNVkit pipeline

from 2.0.CnvkitAccess.sh to 2.3.1.Iamp21CnvkitPlot.sh

Preprocessing to create Theta inputs

• 3.1.CnvkitTheta.sh
• 3.2.CnvkitImportTheta.sh

Gistic pipeline

• 4.1.GisticCnvkitExportSeg.sh
• 4.2.GisticMergeSegment.R
• 4.3.Gistic.sh