XML Variant Ingestion

The ARGO Data Platform supports the ingestion of variant calling data submitted in XML format (based on the GRCh37/hg19 genome reference). These XML files are processed through a standardized workflow to convert them into VCF format, followed by a liftover to the GRCh38 reference genome. For details, please see the latest version of the ARGO xml_variant_ingestion workflow.

Inputs

• Submitted XML file(s): Containing variant calls based on the GRCh37 (hg19) genome reference.
• Metadata mapping file: Used to map identifiers and provide additional sequencing and variant calling context.
• Human reference genome:
  • GRCh38 used as target of liftover
  • GRCh37 used as reference to call variants in the XML file
• Genome liftover chain file: Required for coordinate transformation from GRCh37 to GRCh38.

Processing

1. XML to VCF Conversion:

   • Variant records are parsed from XML and converted into corresponding VCF records.
   • Variants are separated by type:
     • Short Variants: SNVs and InDels
     • Copy Number Alterations (CNVs)
     • Structural Variants / Rearrangements (SVs)

2. Reference Genome Liftover:

   • The converted VCF files are lifted from GRCh37 to GRCh38 using Picard:liftovervcf.

Outputs

• Raw SNV Calls and VCF Index
• Raw Indel Calls and VCF Index
• Raw SV Calls and VCF Index
• Raw CNV Calls and VCF Index

Workflow Diagram