Because Jannovar uses HGVS to describe the variant change in a transcript it is also possible to use HGVS strings and get the genomic position. In Jannovar there is a command line interface to decode a list of HGVS notations into a VCF file.
This is done using the hgvs-to-vcf command. You pass the path to an annotation database that you use in you HGVS code and a file where each line is exactly one HGVS notation. In addition the indexed reference fasta file with a dictionary is needed. The resulting file is a fully supported VCF file.
For example, for converting the small_hgvs.lst file (see small_hgvs.lst) in the examples directory:
# java -jar jannovar-cli-.jar hgvs-to-vcf -d data/hg19_refseq.ser -i examples/small_hgvs.lst -o examples/small_hgvs.vcf -r hg19.fa [...] # ls examples/small_hgvs.vcf small_hgvs.vcf
The file examples/small_hgvs.vcf will look as follows.
##fileformat=VCFv4.2
##ALT=<ID=ERROR,Description="Error in conversion">
##FILTER=<ID=PARSE_ERROR,Description="Problem in parsing original HGVS variant string, written out as variant at 1:g.1N>N">
##INFO=<ID=ERROR_MESSAGE,Number=1,Type=String,Description="Error message">
##INFO=<ID=ORIG_VAR,Number=1,Type=String,Description="Original HGVS variant string from input file to hgvs-to-vcf">
##contig=<ID=1,length=249250621>
#CHROM POS ID REF ALT QUAL FILTER INFO
1 866512 . CC CCCCCT . . .
1 879317 . C T . . .