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.gzVCF File formatvariant_callingSimple Nucleotide VariationSanger WGS Variant Calling, Sanger WXS Variant Calling

Raw SV Calls

Data files containing the structural variation data called from aligned reads, which have not yet been annotated or filtered.

File Types

Filename PatternDescriptionAnalysis TypeData CategoryGenerating Workflow(s)
*.sv.vcf.gzVCF File formatvariant_callingStructural VariationSanger WGS Variant Calling

Raw CNV Calls

Data files containing the copy number segments data called from aligned reads, which have not yet been annotated or filtered.

File Types

Filename PatternDescriptionAnalysis TypeData CategoryGenerating Workflow(s)
*.cnv.vcf.gzVCF file formatvariant_callingCopy Number VariationSanger WGS Variant Calling

Raw InDel Calls

Data files containing the simple insertions and deletions (indels) 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.gzVCF file formatvariant_callingSimple Nucleotide VariationSanger 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_callingSimple Nucleotide Variation, Structural Variation, or Copy Number Variation depending on parent VCFDNA Seq Alignment

Variant Calling Supplement

Data files containing variation results, temporary files, or runtime metric information generated by variant callers used in the ARGO Analysis pipeline.

File Types

Filename PatternDescriptionAnalysis TypeData CategoryGenerating Workflow(s)
*.ascat-supplement.tgzGenerated by Sanger ASCAT CNV caller with bw files removedvariant_calling_supplementCopy Number VariationSanger WGS Variant Calling
*.brass-supplement.tgzGenerated by Sanger BRASS SV caller with bw files and intermediates.tar.gz removedvariant_calling_supplementStructural VariationSanger WGS Variant Calling
*.caveman-supplement.tgzGenerated by Sanger CaVEMan SNV callervariant_calling_supplementSimple Nucleotide VariationSanger WGS Variant Calling, Sanger WXS Variant Calling
*.pindel-supplement.tgzGenerated by Sanger Pindel InDel callervariant_calling_supplementSimple Nucleotide VariationSanger WGS Variant Calling, Sanger WXS Variant Calling
*.timings-supplement.tgzCollected for different processing steps during the Sanger variant callervariant_calling_supplementN/ASanger WGS Variant Calling, Sanger WXS Variant Calling