Convert 'DBexome*.tab' file of the Human Genomic Variation Database http:www.genome.med.kyoto-u.ac.jp/SnpDB/ into 'generic DB file' of the ANNOVAR software package http://www.openbioinfomatics.org/annovar/ . Hgvd2BED generates the 4-column BED file.
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UPDATE (v 0.1.10) HGVD v2.10 has two loci that lack alternetive allele counts at multiple allelic sites at chr2:69093728C>A,G and chr7:1937816C>A,T (both are non-passed sites). Undetermined allele counts are now handled as zero.
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NEW but beta hgvd2vcf.rb converts HGVDr1.42 data into a VCF file. DO NOT USE FOR IMPORTANT PROJECTS.
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UPDATE Supports release version 1.42 (2014.06.17). This release contains new three columns (RR/RA/AA). Newly added loci in this release may have just "." in the filter column. Hgvd2annovar.rb and Hgvd2BED.rb handle them as same as "PASS".
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BUG-FIX (Both Hgvd2annovar and Hgvd2BEDv 0.1.7) For example, in non-biallelic sites, allele frequency of the 2nd alternative allele should have been calculated by "(NA2) / (NR+NA1+NA2+NA3)". However, older version calculated by "(NA2) / (NR+NA2)". This bug overestimated allele frequencies in non-biallelic sites.
Just copy lib/hgvd2annovar.rb lib/hgvd2bed.rb or lib/hgvd2vcf.rb to your working directory. Ruby versions 1.9 or later are recommended.
For your convenience, converted datasets are available in the public_data directory.
ruby hgvd2annovar.rb DBexome20131010.tab > DBexome20131010.tab.txt
ruby hgvd2bed.rb DBexome20131010.tab > DBexome20131010.tab.bed
ruby hgvd2vcf.rb DBexome20131010.tab > DBexome20131010.tab.vcf (no option is supprted)
You can also use an option -a or --all. With these options, output will include non-PASS variants in the filter column.
The output file can be used from ANNOVAR's annotate_variation.pl with options --dbtype generic --genericdbfile DBexome20131010.tab.txt.
In gene-hunting projects, a mistake in variant filtering may cause a disaster. Please recheck results from this script by yourself. The author gratefully welcome your bug reports.
Copyright: © MISHIMA, Hiroyuki, 2013-2015 (hmishima (at) nagasaki-u.ac.jp)
License: The MIT license. See LICENSE.txt for details.