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 Pattern	Description	Analysis Type	Data Category	Generating Workflow(s)
*.snv.vcf.gz	SNV results in VCF File format.	variant_calling	Simple 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 Pattern	Description	Analysis Type	Data Category	Generating Workflow(s)
*.caveman-supplement.tgz	Data files generated by Sanger CaVEMan SNV caller.	variant_calling_supplement	Simple 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 Pattern	Description	Analysis Type	Data Category	Generating Workflow(s)
*.sv.vcf.gz	SV results in VCF File format.	variant_calling	Structural Variation	Sanger 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 Pattern	Description	Analysis Type	Data Category	Generating Workflow(s)
*.brass-supplement.tgz	Data files generated by Sanger BRASS SV caller with bw files and intermediates.tar.gz removed.	variant_calling_supplement	Structural Variation	Sanger 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 Pattern	Description	Analysis Type	Data Category	Generating Workflow(s)
*.cnv.vcf.gz	CNV results in VCF file format.	variant_calling	Copy Number Variation	Sanger 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 Pattern	Description	Analysis Type	Data Category	Generating Workflow(s)
*.ascat-supplement.tgz	Data files generated by Sanger ASCAT CNV caller with bw files removed.	variant_calling_supplement	Copy Number Variation	Sanger 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.

InDel Supplement

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

File Types

Filename Pattern	Description	Analysis Type	Data Category	Generating Workflow(s)
*.pindel-supplement.tgz	Data files generated by Sanger Pindel InDel caller.	variant_calling_supplement	Simple Nucleotide Variation	Sanger WGS Variant Calling Sanger WXS Variant Calling

File Types

Filename Pattern	Description	Analysis Type	Data Category	Generating Workflow(s)
*.indel.vcf.gz	InDel results in VCF file format.	variant_calling	Simple Nucleotide Variation	Sanger WGS Variant Calling Sanger WXS Variant Calling GATK Mutect2 Variant Calling

Filtered SNV Calls

Data files containing Single Nucleotide Variations (SNV) which were filtered through each caller's PASS tag and located only within the open access regions.

File Types

Filename Pattern	Description	Analysis Type	Data Category	Generating Workflow(s)
*.snv.open-filter.vcf.gz	Open access filtered SNV results in VCF File format.	variant_processing	Simple Nucleotide Variation	Open Access Variant Filtering

Filtered InDel Calls

Data files containing the simple Insertions and Deletions (InDel) variants which were filtered through each caller's PASS tag and located only within the open access regions.

File Types

Filename Pattern	Description	Analysis Type	Data Category	Generating Workflow(s)
*.indel.open-filter.vcf.gz	Open access filtered InDel results in VCF file format.	variant_processing	Simple Nucleotide Variation	Open Access Variant Filtering

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 Pattern	Description	Analysis Type	Data Category	Generating Workflow(s)
*.vcf.gz.tbi	VCF Index file format. Requires a corresponding VCF file.	variant_calling variant_processing	Simple Nucleotide Variation Structural Variation Copy Number Variation	Sanger WGS Variant Calling Sanger WXS Variant Calling GATK Mutect2 Variant Calling Open Access Variant Filtering