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  • C elegans known SNPs

    I am planning to analyze some C elegans sequencing data. I have been been trying to find a resource for known SNPs for base recalibration and variant annotation. It seems that this info is not as easy to find as it is for other organisms that I am more familiar with.

    Looks like SNP information is available in WormBase, since there is a "polymorphisms" track in GBrowse. However, I cannot find the raw data anywhere on the FTP site.

    There is also a Wash U SNPs database (http://genome.wustl.edu/services/c-elegans-snpdata/), but that has not been updated since 2001.

    I am ideally looking for a VCF file for build WS220 (UCSC ce10), but any info would be much appreciated.

  • #2
    This data is probably in one of the GFF files on the wormbase ftp site but one way to download it is by clicking on the "floppy" icon (third from right) in the polymorphisms track (see attached graphics). You can then choose to download variants from an area/a chromosome/entire genome in Fasta/Genbank/GFF3 format.
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