Convert HGVS to VCF

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-0.19.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       .       .       .