DNA-Seq Alignment

The ARGO Data Platform accepts raw sequencing data in both FASTQ and BAM (aligned or unaligned) format. The first processing step in the DNA-Seq Pipeline is uniformly aligning samples to the GRCh38 reference genome. For details, please see the latest version of the ARGO DNA-Seq Alignment.

Inputs

• All alignments are performed using GRCh38DH as the human reference genome
• Submitted FASTQ or BAM files(s)

Preprocessing

• Submitted sequencing reads (FASTQ or BAM) are converted into lane level (i.e read group level) BAMs.
• Picard:CollectQualityYieldMetrics is used for read group level BAM QC.

Processing

• BWA-MEM (version 0.7.17-r1188) is performed to map the reads to the reference genome for each read group.
• Biobambam2 (version 2.0.153) is used to merge all read group level mapped BAMs into sample level BAM and mark duplicates per library.
• Samtools:stats is used to calculate Alignment QC metrics.
• Picard:CollectOxoGMetrics is used to calculate the OxoQ score for oxidative artifact assessment.

Outputs

• Aligned Reads CRAM and Aligned Reads Index
• QC metrics files
  • Alignment Metrics files
  • OxoG Metrics files
  • Duplicates Metrics files
  • Read Group Metrics files for each submitted read group

Workflow Diagram