⚠️ Currently, only repeat expansion VCF files produced by Oxford Nanopore are supported.
VarSome Clinical can annotate short tandem repeats (STR) VCF files. The VCFs uploaded to annotate STRs must meet the following requirements:
- Are compliant with the VCF standard.
- The number of repeats is shown in the ALT field as < STRn > where n is the number of repeats.
- The INFO field contains the repeat unit in the following format: DisplayRU=CCG, SVTYPE=STR, STR_NORMAL_MAX=NN, STR_PATHOLOGIC_MIN=NNN, STR_STATUS=N
- The FORMAT field contains the number of repeats spanned by each allele.
##FORMAT=<ID=CN,Number=A,Type=Integer,Description="Number_of_repeat_units_spanned_by_the_allele">An example of a VCF header + its corresponding variant would be the following
##fileformat=VCFv4.3
##reference=/ref/genomes/hg19/hg19.fa
##ALT=<ID=.,Description="repeat expansion (insertion)">
##INFO=<ID=Disease,Number=1,Type=String,Description="Associated_disorder">
##INFO=<ID=DisplayRU,Number=1,Type=String,Description="Display_repeat_unit_familiar_to_clinician">
##INFO=<ID=InheritanceMode,Number=1,Type=String,Description="Main_mode_of_inheritance_for_disorder">
##INFO=<ID=REF,Number=1,Type=Integer,Description="Reference_copy_number">
##INFO=<ID=RU,Number=1,Type=String,Description="Repeat_unit_in_the_reference_orientation">
##INFO=<ID=STR_NORMAL_MAX,Number=1,Type=Integer,Description="Max_number_of_repeats_allowed_to_call_as_normal">
##INFO=<ID=STR_PATHOLOGIC_MIN,Number=1,Type=Integer,Description="Min_number_of_repeats_required_to_call_as_pathologic">
##INFO=<ID=STR_STATUS,Number=A,Type=String,Description="Repeat_expansion_status._Alternatives_in_[normal,_pre_mutation,_full_mutation]">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type_of_structural_variant">
##FORMAT=<ID=CN,Number=A,Type=Integer,Description="Number_of_repeat_units_spanned_by_the_allele">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##ALT=<ID=STR10,Description="Allele_comprised_of_10_repeat_units">
##ALT=<ID=STR2,Description="Allele_comprised_of_2_repeat_units">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
chrX 147912050 . G <STR32> . . Disease=FragileX;DisplayRU=CGG;InheritanceMode=XR;REF=20;RU=GGC;STR_NORMAL_MAX=55;STR_PATHOLOGIC_MIN=200;STR_STATUS=normal;SVTYPE=DUP GT:CN 0/1:32
chrX 147912050 . G <STR881> . . Disease=FragileX;DisplayRU=CGG;InheritanceMode=XR;REF=20;RU=GGC;STR_NORMAL_MAX=55;STR_PATHOLOGIC_MIN=200;STR_STATUS=full_mutation;SVTYPE=DUP GT:CN 1/0:881
The STR analysis from VCF is launched as a sub-analysis of the main analysis. You can launch a STR annotation by:
- Adding an STR VCF file when defining your sample.
- Launching the analysis once the main analysis has finished as a “New Repeat Expansion sub-analysis” either from single or multi sample analyses.
