Hi,

I am performing filter based annotation using Annovar for my vcf file generated using GATK4.

The command used is:

annotate_variation.pl -filter -out sample -build hg19 -dbtype clinvar_20221231  sample.avinput humandb/

The output I got the following output:

clinvar_20221231        192257  1       100316       100317       C       G       1       100316       .       C       G       250.64  filter  AC=1;AF=0.500;AN=2;BaseQRankSum=1.35;DP=24;ExcessHet=0.0000;FS=3.949;MLEAC=1;MLEAF=0.500;MQ=57.00;MQRankSum=0.00;QD=10.44;ReadPosRankSum=-1.402e+00;SOR=0.552  GT:AD:DP:GQ:PL  0/1:15,9:24:99:258,0,406

According to Annovar documentation the output I am supposed to get is in this format:

clinvar_20140211 CLINSIG=other|other;CLNDBN=Inflammatory_bowel_disease_17\x2c_protection_against|Psoriasis\x2c_protection_against;CLNACC=RCV000003254.2|RCV000003255.2 1 67705958 67705958 G A comments: rs11209026 (R381Q), a SNP in IL23R associated with Crohn's disease
clinvar_20140211 CLINSIG=pathogenic|pathogenic|pathogenic|pathogenic;CLNDBN=Deafness\x2c_autosomal_recessive_1A|Deafness\x2c_digenic\x2c_GJB2/GJB6|Hereditary_hearing_loss_and_deafness|not_provided;CLNACC=RCV000018527.27|RCV000018528.27|RCV000037843.1|RCV000080373.1 13 20763686 20763686 comments: rs1801002 (del35G), a frameshift mutation in GJB2, associated with hearing loss
clinvar_20140211 CLINSIG=other;CLNDBN=Inflammatory_bowel_disease_1\x2c_susceptibility_to;CLNACC=RCV000004957.1 16 50745926 50745926 comments: rs2066844 (R702W), a non-synonymous SNP in NOD2

Compared to this my output file does not have any information such as CLINSIG, CLNDBN etc. rather than a 6 digit number. When I checked this number in ClinVar database it shows a different variant in a different position.

I would like to know how can I get the information mentioned in the documentation.

Thank you.