We aligned all wild isolate genomes to the WS245 version of the N2 genome. These data are stored using the BAM and CRAM formats. CRAM files are substantially smaller than BAM files.
CRAM files are substantially smaller than BAM files, but require the reference to be converted to BAM files. We are currently using WS245 (Download).
Downloading All Alignment Data
Interested in downloading everything? Use the scripts below! Before these scripts will work, you need to download and install wget. We recommend using Homebrew for this installation (Unix/Mac OS), or Cygwin on windows. See the FAQ for details on installing wget.
We used samtools to identify single-nucleotide variant (SNV) sites as compared to the N2 reference genome (WS245). Variant data are provided as VCF or tab-delimited files.
The file below is a single VCF containing SNVs for all wild isolates.
You can also access specific regions of VCF files (rather then the entire file) from the command line:
Information regarding alignment, variant calling, and annotation are available here.
Download Strain Data
Currently, we have performed variant calling across all wild isolates. We are working to add additional variant classes including insertion/deletion, structural, transposon, and additional variant classes.
We have recently performed an anaysis characterizing Transposon variation in C. elegans. The dataset will be further integrated with the site resources as time goes on. For now, the raw data are available below.Download Transposon Data
The following statistics were generated with
bcftools stats. The soft-filtered VCF for this release has had records and genotypes annotated but no data has been removed. The hard-filtered VCF removes records and genotypes that have been annotated with filters.
The hard-filtered VCF has stripped records and genotypes that have had filters applied.