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This article mainly introduces the example analysis of clinvar database, which is very detailed and has certain reference value. Friends who are interested must finish it!

Clinvar database

Clinvar is an open database to which each research institution can submit data, and a team of experts will review and rate the submitted information. The sites in the database are divided into 1 to 4 different stars according to the reliability of the annotation information. the higher the star level is, the higher the credibility is.

Database address: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh47/

If you install ANNOVAR, you can download it directly:

Perl annotate_variation.pl-downdb-buildver hg19-downdb-webfrom annovar clinvar_20180603. /

After downloading, you get some comment information. ANNOVAR contains five comment information: CLNALLELEID, CLNDN, CLNDISDB, CLNREVSTAT, CLNSIG:

ALLELEID = "the ClinVar Allele ID" CLNDN = "ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB" CLNDNINCL = "For included Variant: ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB" CLNDISDB = "Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN" CLNDISDBINCL = "For included Variant: Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN" CLNHGVS = "Top-level (primary assembly, alt) Or patch) HGVS expression. "CLNREVSTAT =" ClinVar review status for the Variation ID "CLNSIG =" Clinical significance for this single variant "

Where CLNDSDB refers to the database from which the record comes from.

Latest database updates:

Sometimes the clinvar database is updated quickly, and the official comment file provided by ANNOVAR may not be timely. We can download the data ourselves and use the script provided by ANNOVAR to make the comment file of clinvar:

Preparatory work:

1. First install vt: https://genome.sph.umich.edu/wiki/Vt#Installation if you report a mistake: https://www..com/article/461

two。 Download the script prepare_annovar_user.pl from: http://www.openbioinformatics.org/annovar/download/prepare_annovar_user.pl

The command line is as follows:

Export PATH=/share/work/biosoft/annovar/2018Apr16/annovar:/share/work/biosoft/vt/vt-0.57721/:$PATHwget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh47/clinvar_20180805.vcf.gzwget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh47/clinvar_20180805.vcf.gz.tbivt decompose clinvar_20180805.vcf.gz-o temp.split.vcfprepare_annovar_user.pl-dbtype clinvar_preprocess2 temp .split.vcf-out temp.split2.vcfvt normalize temp.split2.vcf-r.. /.. / GRCH37/Homo_sapiens.GRCh47.dna.toplevel.fa-o temp.norm.vcf-w 2000000prepare_annovar_user.pl-dbtype clinvar2 temp.norm.vcf-out hg19_clinvar_20180805.txt#index_annovar.pl hg19_clinvar_20180805_raw.txt-out hg19_clinvar_20180805.txt-comment comment_20180805.txt

Finally: the index_annovar.pl script can not be found, in fact, the file is not large, it may not be indexed.

The above is all the contents of the article "sample Analysis of clinvar Database". Thank you for reading! Hope to share the content to help you, more related knowledge, welcome to follow the industry information channel!

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