Variant Calls

ICGC ARGO provides access to data from ARGO member programs generated through the standardized ARGO Analysis pipelines. The following page lists variant calling analyses and data files generated by the ARGO Analysis pipelines.

Raw SNV Calls

Data files containing Single Nucleotide Variations (SNV) called from aligned reads, which have not yet been annotated but do have some filtering flags added.

File Types

Filename PatternDescriptionAnalysis TypeData CategoryGenerating Workflow(s)
*.snv.vcf.gzSNV results in VCF File format.variant_callingSimple Nucleotide Variation
  • Sanger WGS Variant Calling
  • Sanger WXS Variant Calling
  • GATK Mutect2 Variant Calling

SNV Supplement

Data files containing SNV results and temporary files generated by variant callers used in the ARGO Analysis pipeline.

File Types

Filename PatternDescriptionAnalysis TypeData CategoryGenerating Workflow(s)
*.caveman-supplement.tgzData files generated by Sanger CaVEMan SNV caller.variant_calling_supplementSimple Nucleotide Variation
  • Sanger WGS Variant Calling
  • Sanger WXS Variant Calling

Raw SV Calls

Data files containing Structural Variations (SV) called from aligned reads, which have not yet been annotated or filtered.

File Types

Filename PatternDescriptionAnalysis TypeData CategoryGenerating Workflow(s)
*.sv.vcf.gzSV results in VCF File format.variant_callingStructural VariationSanger WGS Variant Calling

SV Supplement

Data files containing SV results and temporary files generated by variant callers used in the ARGO Analysis pipeline.

File Types

Filename PatternDescriptionAnalysis TypeData CategoryGenerating Workflow(s)
*.brass-supplement.tgzData files generated by Sanger BRASS SV caller with bw files and intermediates.tar.gz removed.variant_calling_supplementStructural VariationSanger WGS Variant Calling

Raw CNV Calls

Data files containing the Copy Number Varations (CNV) called from aligned reads, which have not yet been annotated or filtered.

File Types

Filename PatternDescriptionAnalysis TypeData CategoryGenerating Workflow(s)
*.cnv.vcf.gzCNV results in VCF file format.variant_callingCopy Number VariationSanger WGS Variant Calling

CNV Supplement

Data files containing CNV results and temporary files generated by variant callers used in the ARGO Analysis pipeline.

File Types

Filename PatternDescriptionAnalysis TypeData CategoryGenerating Workflow(s)
*.ascat-supplement.tgzData files generated by Sanger ASCAT CNV caller with bw files removed.variant_calling_supplementCopy Number VariationSanger WGS Variant Calling

Raw InDel Calls

Data files containing the simple insertions and deletions (InDel) data called from aligned reads, which have not yet been annotated but do have some filtering flags added.

File Types

Filename PatternDescriptionAnalysis TypeData CategoryGenerating Workflow(s)
*.indel.vcf.gzInDel results in VCF file format.variant_callingSimple Nucleotide Variation
  • Sanger WGS Variant Calling
  • Sanger WXS Variant Calling
  • GATK Mutect2 Variant Calling

InDel Supplement

Data files containing InDel results and temporary files generated by variant callers used in the ARGO Analysis pipeline.

File Types

Filename PatternDescriptionAnalysis TypeData CategoryGenerating Workflow(s)
*.pindel-supplement.tgzData files generated by Sanger Pindel InDel caller.variant_calling_supplementSimple Nucleotide Variation
  • Sanger WGS Variant Calling
  • Sanger WXS Variant Calling

VCF Index

Secondary files that are external index files for VCF format files. TBI files follow a naming convention that corresponds to their matching VCF file of the original filename suffixed with .vcf.gz.tbi. Index files are required for selective access to genomic data inside a VCF file.

File Types

Filename PatternDescriptionAnalysis TypeData CategoryGenerating Workflow(s)
*.vcf.gz.tbiVCF Index file format. Requires a corresponding VCF file.variant_calling
  • Simple Nucleotide Variation
  • Structural Variation
  • Copy Number Variation
  • Sanger WGS Variant Calling
  • Sanger WXS Variant Calling
  • GATK Mutect2 Variant Calling