Data Releases

C. elegans releases



Release Summary
  • Strains: 552
  • WGS strains: 413
  • Isotypes: 249
  • Genome: WS258

Alignment Data

Wild isolate genomes are aligned and stored using the BAM format. BAMs are available in the table below.

Downloading All Alignment Data

You can download all alignment data using the script below. Before this script 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.

download_bams.sh

Methods

Information regarding alignment, variant calling, and annotation are available here.

Variant Data

We used samtools to identify single-nucleotide variant (SNV) sites as compared to the N2 reference genome. Variant data are provided as VCF or tab-delimited files.

VCF

VCFs generated from the variant calling pipeline are provided below.

  • Soft-filter - Includes all variants and annotations. The QC status of variants is included.
  • Hard-filter - Variants and genotypes that fail QC are removed.
  • Imputed - An imputed dataset generated from the hard-filter VCF.

You can programmatically access specific regions of VCF files (rather then the entire file) from the command line:


Strain Data
Strain Data including isolation location, isotype information, and more is available for download.

Download Strain Data

Included Variants

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.

Transposon Data

We have recently performed an analysis 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
# Reference Strain Isotype Strains Isotype BAM Tab-delimited variants


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.

Variable Soft-Filtered Hard-Filtered
Samples 249 249
SNVs 2,434,802 1,865,541
Ts 1,361,672 1,041,676
Tv 1,153,388 823,865
Ts/Tv 1.18 1.26
These numbers reflect the number of variants in the entire CaeNDR C. elegans population.

Methods

Note: These methods operated on sequence data at the isotype level.

Software

Alignment

Sequences were aligned to WS245 using BWA (version 0.7.8-r455). Optical/PCR duplicates were marked with PICARD (version 1.111).

Variant Calling

SNV calling was performed using bcftools (version 1.3).

Filtering

Sites with greater than 10% missing or greater than 90% heterozygous calls across all isotypes were removed. Individual calls with the following parameters were removed:

  • Depth of coverage (DP) <= 10
  • Quality (QUAL) < 30
  • Mapping Quality (MQ) < 40. Only applied to ALT calls.
  • Number of high-quality non-reference bases (DV) / Depth of Coverage (DP) < 0.5. Applied only to ALT calls.

Annotation

Variants were annotated using SnpEff (version 4.1g) using the WS241 database.

Pipelines

The C. elegans Natural Diversity Resource has three git repos which contain the software used to run the site.

AndersenLab/cegwas

A set of functions to process phenotype data, perform GWAS, and perform post-mapping data processing for C. elegans.

AndersenLab/cegwas-worker

A python daemon that handles submitted mapping jobs from base. cegwas-worker Runs on Google Compute Engine.

AndersenLab/CeNDR

The software responsible for this website, which is run using Google App Engine.

Haplotypes

Click the above image to download the full version