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Annotations VCF File Format

While JSON output format is the default option, we support VCF file as our output too. The VCF output format can be enabled by --output-format vcf as shown below:

dotnet Annotator.dll \
     -c Data/Cache \
     --output-format vcf \
     -r Data/References/Homo_sapiens.GRCh38.Nirvana.dat \
     -i HiSeq.10000.vcf.gz \
     -o HiSeq.10000.out
# HiSeq.10000.out.vcf.gz file should be produced after processing.

VCF Output Format

Header

The output VCF file should have headers similar as below, which indicates the Illumina Connected Annotations' version, file creation time, assembly, and data sources used for producing the output:

##fileformat=VCFv4.2
##IlluminaConnectedAnnotations="3.24.0" time="2024-03-22 07:02:13" assembly="GRCh38" Ensembl="110" RefSeq="GCF_000001405.40-RS_2023_03"
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20230110
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
...
##INFO=<ID=CTB,Number=1,Type=String,Description="Cytoband of the position">
##INFO=<ID=NOM,Number=.,Type=String,Description="Simple ISCN-like nomanclature for each of the variants">
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Illumina Connected Annotations. Format: Allele|Consequence|GeneSymbol|FeatureType|Feature|Canonical|HGVSg|HGVSc|HGVSp|VariantId|Impact|GeneNcbiId|CompleteOverlap|BioType">
...
##FORMAT=<ID=SNOM,Number=1,Type=String,Description="SNOM of the sample">
...
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  Novaseq_TSPF450-NA12878-1-HFHWJDMXX_S1_L001     Novaseq_TSPF450-NA12891-1-HFHWJDMXX_S3_L001

VCF Lines

Core annotation for overlapping transcripts is enabled and no supplementary annotation is added in VCF mode. CSQ and CTB fields under INFO column and SNOM Sample field are added with following format:

Multiple transcripts are separated with ,. An example of produced VCF lines as below:

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