UCSC2VCF
WARNING!
The author knows that if a broken VCF file is used for an important project to filter-out potential variants, it results a CATASTROPHE. This is a MIT-licensed software. Use at your own risk ;-)
Motivation
UCSC curates NCBI's dbSNP data before release at the UCSC Genome Database. However, only NCBI releases the dbSNP information in the VCF format. If you need UCSC-curated dbSNP information (dbSNP13x, dbSNP13xCommon, etc.) in the VCF format, you have to do that by yourself.
Dependency
gem install bio
gem install bio-ucsc-api
gem install striuct
Input file preparation
- download reference sequence in the 2bit file format. For example, the human hg19 reference sequence is available at http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit
- download UCSC's dbSNP table using "Table Browser". Select "Group: Variation and Repeats" and "All SNPs (135)" or your favorite database. Then select "genome", select "all fields from selected table", and download (using gzip compress is better).
- The VCF header is hard-coded in the script. Please change it if you do not use dbSNP135.
How to use
ucsc2vcf -r reference.2bit --snv --indel hg19_snp135.txt > results.vcf
zcat hg19_snp135.txt.gz | ucsc2vcf -r reference.2bit --snv --indel > results.vcf
--snv
outputs "single nucleotide -> single nucleotide substitutions". Can be combined with--indel
.--indel
outputs " '-' to nucleotide(s) or nucleotide(s) to '-' substitutions". Can be combined with--snv
.- Other variations such as large indels (allels are not [-ATGC]) are all ignored.
Copyright
MISHIMA, Hiroyuki (hmishima at nagasaki-u.ac.jp, @mishimahryk at Twitter), 2012-2017