This directory contains a sorted and gzip-compressed VCF (Variant Call Format)
file containing all germline variations from the current EnsemblGenomes
release for this species, named ixodes_scapularis.vcf.gz. Variations that have been
failed by the EnsemblGenomes QC checks are not included. However, we provide
GVF dumps for failed variations.

If this species has any structural variation data this is provided in a file
named ixodes_scapularis_structural_variations.vcf.gz.

A file including the consequences of the variations on the EnsemblGenomes
transcriptome, as called by the variation consequence pipeline, can be found
in a file called ixodes_scapularis_incl_consequences.vcf.gz.

The data contained in these files is presented in VCF format. For more
details about the format refer to:
http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41

For various reasons it may be necessary to store information about a variation that has failed quality checks in the Variation pipeline. Variations can be considered to be "failed_variations" for the following reasons:

- Variation maps to more than 3 different locations
- None of the variant alleles match the reference allele
- Variation has more than 3 different alleles
- Loci with no observed variant alleles in dbSNP
- Variation does not map to the genome
- Variation has no genotypes
- Genotype frequencies do not add up to 1
- Variation has no associated sequence
- Variation submission has been withdrawn by the 1000 genomes project due to high false positive rate
- Additional submitted allele data from dbSNP does not agree with the dbSNP refSNP alleles
- Variation has more than 3 different submitted alleles
- Alleles contain non-nucleotide characters
- Alleles contain ambiguity codes
- Mapped position is not compatible with reported alleles
- Variation can not be re-mapped to the current assembly
- Supporting evidence can not be re-mapped to the current assembly
- Flagged as suspect by dbSNP
- Variation maps to more than one genomic location

Keeping track of failed variations can be used as a way to check why some variations that were present in the dataset mapped to the genome are not to be found anywhere on the genome. These failed variations are stored in the file ixodes_scapularis_failed.vcf.gz.

Questions about these files can be addressed to the Ensembl helpdesk:
helpdesk@ensembl.org, or to the developer's mailing list: dev@ensembl.org.