How to replace the clinvar_20190305 with the newest version clinvar_20210609?
lincj1994 opened this issue · 1 comments
lincj1994 commented
Hi, I found that InterVar calls the clinvar_20190305. I dont know how to replace it with the newest version of 20210609 downloaded from clinvar ftp?
In humandb folder, there are two clinvar-related files (hg19_clinvar_20190305.txt, hg19_clinvar_20190305.txt.idx), and the head of hg19_clinvar_20190305.txt was like this.
#Chr | Start | End | Ref | Alt | CLNALLELEID | CLNDN | CLNDISDB | CLNREVSTAT | CLNSIG
-- | -- | -- | -- | -- | -- | -- | -- | -- | --
1 | 949422 | 949422 | G | A | 446939 | Immunodeficiency_38_with_basal_ganglia_calcification | MedGen:C4015293\x2cOMIM:616126\x2cOrphanet:ORPHA319563 | criteria_provided\x2c_single_submitter | Benign
1 | 949502 | 949502 | C | T | 514926 | Immunodeficiency_38_with_basal_ganglia_calcification | MedGen:C4015293\x2cOMIM:616126\x2cOrphanet:ORPHA319563 | criteria_provided\x2c_single_submitter | Uncertain_significance
1 | 949523 | 949523 | C | T | 181485 | Immunodeficiency_38_with_basal_ganglia_calcification | MedGen:C4015293\x2cOMIM:616126\x2cOrphanet:ORPHA319563 | no_assertion_criteria_provided | Pathogenic
1 | 949559 | 949559 | C | T | 514896 | Immunodeficiency_38_with_basal_ganglia_calcification | MedGen:C4015293\x2cOMIM:616126\x2cOrphanet:ORPHA319563 | criteria_provided\x2c_single_submitter | Uncertain_significance
1 | 949597 | 949597 | C | T | 446987 | Immunodeficiency_38_with_basal_ganglia_calcification | MedGen:C4015293\x2cOMIM:616126\x2cOrphanet:ORPHA319563 | criteria_provided\x2c_single_submitter | Benign
1 | 949608 | 949608 | G | A | 389314 | not_specified | MedGen:CN169374 | criteria_provided\x2c_single_submitter | Benign
I wonder if I could replace this file with the same format of clinvar_20210609.vcf.gz and keep the hg19_clinvar_20190305.txt.idx?
quanliustc commented
we are doing update for the new version of clinvar, you also can download most updated clinvar data file from annovar and then replace it.