HGVDinHg38

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Hiroyuki MISHIMA edited this page Sep 17, 2015 · 5 revisions

Liftover HGVD allele frequency DB

Participants: @misshie
Human Genetic Variation Database of the Japanese 1200 exome dataset at http://www.genome.med.kyoto-u.ac.jp/SnpDB/
Original data uses the hg19 coordination

Protocol

HGVD was converted into a VCF file. See https://github.com/misshie/hgvd2annovar
Use CrossMap at http://crossmap.sourceforge.net/ to perform automatic liftover

Using CrossMap, 1,006 loci in 478,228 loci were unmapped.

Validate result in-house scripts using Ruby UCSC API at https://github.com/misshie/bioruby-ucsc-api .
In SNV sites (total 468,025), REF sequences in 5 sites are discordant to hg38.
In unmapped 1,006 loci, 639 loci has dbSNP142-registered with single positions. Thus, 367 loci may need BLAT remapping.