README.md

Data pre-processing for variant discovery GATK4

An HPC workflow that pre-processes 50 matched tumor-normal whole genome sequencing (WGS) fastq files from 25 childhood acute lymphoblastic leukemia cases. WGS data were from Illumina NovaSeq 6000 Sequencing. Check out gatk doc for more details.

This workflow was written according to the following GATK official WDLs:

• Detailed versions:
  • https://github.com/gatk-workflows/gatk4-genome-processing-pipeline/blob/master/tasks/UnmappedBamToAlignedBam.wdl
  • https://github.com/gatk-workflows/gatk4-genome-processing-pipeline/blob/master/WholeGenomeGermlineSingleSample.wdl
• Simple version:
  • https://github.com/gatk-workflows/gatk4-data-processing/blob/master/processing-for-variant-discovery-gatk4.wdl
  • Detailed documents for this simple version: https://github.com/broadgsa/gatk/blob/master/doc_archive/methods/Reference_implementation:_PairedEndSingleSampleWf_pipeline.md#SortAndFixTags
• Other tutorials:
  • A practical introduction to GATK 4 on Biowulf (NIH HPC)
  • (howto) Recalibrate base quality scores = run BQSR

The main steps in the preprocessing workflow. A figure from GITC.

Step 0: QC

• 0.1.Fastqc.sh

Step 1: Fastqs to Unmapped BAMs

• 1.1.PairedFastqToUnmappedBam.sh
• 1.2.ValidateSamFile.sh
• 1.3.SortSam.sh

Step 2: Unmapped BAMs to Mapped BAMs

• 2.1.Bwa.sh
• 2.2.SortAlignedBam.sh
• 2.3.ValidateAlignedBam.sh
• 2.4.CheckIfAltAwareAlign.sh

Step 3: Merge Unmapped BAMs and Mapped BAMs

• 3.1.MergeBamAlignment.sh
• 3.2.ValidateMergedBam.sh
• 3.3.CountReads.sh

Step 4: MarkDuplicates

• 4.1.MarkDuplicates.sh
• 4.2.SortAndFixTags.sh
• 4.3.ValidateSortedMarkedBam.sh

Step 5: Base Quality Score Recalibration

• 5.1.BaseRecalibrator.sh
• 5.2.BqsrPlot.sh
• 5.3.BqsrPlot.Rmd