High-Quality Zebrafish Dbsnp Database

Question

[michealsmith]

How to download zebrafish dbSNP database, in vcf format at the best?

I've checked UCSC: http://genome.ucsc.edu/cgi-bin/hgTables?org=Zebrafish&db=danRer7&hgsid=255390817&hgta_doMainPage=1) It's werid there's no dbSNP column for fish; while we do have for human.

Also, a silly question: Can I download dbSNP database from dbSNP NCBI website? http://www.ncbi.nlm.nih.gov/projects/SNP/ We can search for certain SNP, but how can I download the whole package? thx

Answer 1

[Pierre Lindenbaum]

The dbSNP files (XML, ASN1 flat, database dumps...) for zebrafish are available under: ftp://ftp.ncbi.nih.gov/snp/organisms/zebrafish_7955/

EDIT: you could download the XML genotype files: eg: ftp://ftp.ncbi.nih.gov/snp/organisms/zebrafish_7955/genotype/gt_chr1.xml.gz

and apply the following stylesheet (not tested , is there a +0/+1 shift ?)

<xsl:stylesheet xmlns:xsl="&lt;a href="http://www.w3.org/1999/XSL/Transform" "="" rel="nofollow">http://www.w3.org/1999/XSL/Transform'
    xmlns:g="http://www.ncbi.nlm.nih.gov/SNP/geno"
    version='1.0'
    >



<xsl:output method="text" encoding="UTF-8"/>


<xsl:template match="/">
<xsl:text>##fileformat=VCFv4.1
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT
</xsl:text>
<xsl:apply-templates select="g:GenoExchange/g:SnpInfo"/>
</xsl:template>


<xsl:template match="g:SnpInfo">
<xsl:variable name="ID" select="concat('rs',@rsId)"/>
<xsl:variable name="obs" select="@observed"/>
<xsl:for-each select="g:SnpLoc">
<xsl:value-of select="@chrom"/>
<xsl:text>  </xsl:text>
<xsl:value-of select="@start"/>
<xsl:text>  </xsl:text>
<xsl:value-of select="$ID"/>
<xsl:text>  .   </xsl:text>
<xsl:value-of select="$obs"/>
<xsl:text>  .   .   .   .</xsl:text>
<xsl:text>
</xsl:text>
</xsl:for-each>
</xsl:template>


</xsl:stylesheet>

transform:

 xsltproc stylesheet.xsl  gt_chr1.xml

result:

##fileformat=VCFv4.1
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT
1   22877360    rs3727476   .   C/T .   .   .   .
1   22878686    rs3727477   .   C/T .   .   .   .
1   22878722    rs3727478   .   C/T .   .   .   .
1   2356878 rs3727479   .   A/G .   .   .   .
1   2356516 rs3727480   .   C/G .   .   .   .
1   2356545 rs3727481   .   A/T .   .   .   .
1   2356590 rs3727482   .   C/T .   .   .   .
1   2356695 rs3727483   .   A/G .   .   .   .
1   2356816 rs3727484   .   A/G .   .   .

.

[michealsmith]

thx, I definitely have seen this. But seems it doesn't contain vcf format...where can I find vcf format?