Annotating VCF Files

The main purpose of Jannovar is the annotation of all variants in a VCF file. That is, for each annotation, predict the results for all transcripts that can be afflicted by the change. Depending on the configuration, the one effect that is most pathogenic, or all, are written out.

This is done using the annotate command. You pass the path to an annotation database and one or more paths to VCF files that are to be annotated. For each file, the resulting annotated file is to the current directory, the file name is derived by replacing the file name suffix .vcf to .jv.vcf.

For example, for annotating the small.vcf file in the examples directory:

# java -jar jannovar-cli-0.11.jar annotate data/hg19_ucsc.ser examples/small.vcf
[...]
# ls
[...]
small.jv.vcf

The first three variant lines of small.jv.vcf will look as follows.:w

1 866511  rs60722469      C       CCCCT   258.62  PASS    EFFECT=INTRONIC;HGVS=SAMD11:NM_152486.2:c.305+42_305+43insCCCT  GT:AD:DP:GQ:PL  1/1:6,5:11:14.79:300,15,0
1 879317  rs7523549       C       T       150.77  PASS    EFFECT=MISSENSE;HGVS=SAMD11:XM_005244727.1:exon9:c.799C>T:p.Arg267Cys   GT:AD:DP:GQ:PL  0/1:14,7:21:99:181,0,367
1 879482  .       G       C       484.52  PASS    EFFECT=MISSENSE;HGVS=SAMD11:XM_005244727.1:exon9:c.964G>C:p.Asp322His   GT:AD:DP:GQ:PL  0/1:28,20:48:99:515,0,794

The Show-All Option

By default, Jannovar will only write out one most pathogenic variant as predicted. You can use the --show-all/-a option to write out all functional annotations:

# java -jar jannovar-cli-0.11.jar annotate --show-all data/hg19_refseq.ser examples/small.vcf

For example, the first line of small.jv.vcf will look as follows and contain multiple effects and HGVS annotations.

1   866511  rs60722469      C       CCCCT   258.62  PASS    EFFECT=INTRONIC,INTRONIC,INTRONIC,INTRONIC,INTRONIC,INTRONIC,ncRNA_INTRONIC,ncRNA_INTRONIC;HGVS=SAMD11:NM_152486.2:c.305+42_305+43insCCCT,SAMD11:XM_005244723.1:c.305+42_305+43insCCCT,SAMD11:XM_005244724.1:c.305+42_305+43insCCCT,SAMD11:XM_005244725.1:c.305+42_305+43insCCCT,SAMD11:XM_005244726.1:c.305+42_305+43insCCCT,SAMD11:XM_005244727.1:c.305+42_305+43insCCCT,SAMD11:XR_241028.1:n.661+42_661+43insCCCT,SAMD11:XR_241029.1:n.661+42_661+43insCCCT  GT:AD:DP:GQ:PL  1/1:6,5:11:14.79:300,15,0