Sanger WXS Variant Calling

Whole exome sequencing (WXS) aligned CRAM files are processed through the Sanger WXS Variant Calling Workflow as tumour/normal pairs. The ARGO DNA Seq pipeline has adopted the Sanger Whole Exome Sequencing Analysis Docker Image as the base workflow. For details, please see the latest version of the ARGO Sanger WXS Variant Calling workflow.

Inputs

• Normal WXS aligned CRAM and index files
• Tumour WXS aligned CRAM and index files
• Reference files

Processing

• Pindel InDel caller is used for somatic insertion/deletion variant detection.
• CaVEMan SNV caller is used for somatic single nucleotide variant analysis.

Collect QC Metrics

• WXS aligned reads statistics are generated by Sanger:bam_stats script. The files containing normal/tumour aligned reads statistics are further used by Pindel caller.

Outputs

• Raw SNV Calls and VCF Index
• Raw InDel Calls and VCF Index
• SNV Supplement files
• InDel Supplement files
• QC Metrics
  • Alignment Metrics for both the Tumour and Normal samples
  • Runtime Stats

Workflow Diagram