How can I annotate with dbsnp and also include info fields from dbsnp vcf?
I want to annotate my vcf using dbsnp, however I don't want to add only the dbsnp rs#s in the ID field. I also want to add INFO fields from the dbsnp vcf into the annotated vcf. How can this be achieved?
I tried to do it by running the command below, but this did not work.
java -jar GenomeAnalysisTK.jar \ -R ucsc.hg19.fasta \ -T VariantAnnotator \ -V gatk.vcf \ -o gatk_dbsnp138.vcf \ --dbsnp dbsnp_138.hg19.vcf \ --resource:dbsnp dbsnp_138.hg19.vcf \ --expression dbsnp.CLNSIG \ --expression dbsnp.CLNACC
Thanks very much,