This directory contains sorted and bgzip-compressed VCF (Variant Call Format) files:

    From release/93 we dump data per chromosome (1-22, MT, X, Y) for:
    homo_sapiens-chr*.vcf.gz
        All germline variations from the current Ensembl release for this
        species
    homo_sapiens_incl_consequences-chr*.vcf.gz
        All consequences of the variations on the Ensembl transcriptome,
        as called by the variation consequence pipeline

    homo_sapiens_structural_variations.vcf.gz
        All structural variations (if available for this species)
    homo_sapiens_somatic.vcf.gz
        All somatic mutations from the current Ensembl release.
    homo_sapiens_somatic_incl_consequences.vcf.gz
        All consequences of somatic mutations on the Ensembl transcriptome,
        as called by the variation consequence pipeline
    homo_sapiens_phenotype_associated.vcf.gz
        All variations from the current Ensembl release that have been
        associated with a phenotype
    homo_sapiens_clinically_associated.vcf.gz
        All variations from the current Ensembl release that have been
        described by ClinVar as being probable-pathogenic, pathogenic,
        drug-response or histocompatibility

Additionally, we provide for human:
    - files containing allele frequencies from 1000 genomes phase 3 populations
      and from populations from the Exome Sequencing Project
    - NOTE: files containg allele frequencies from several of the HapMap
      populations have been discontinued and are available from our archive sites,
      the latest being ftp://ftp.ensembl.org/pub/release-97/variation/vcf/homo_sapiens/
If available for this species, the file includes information on:
    - ancestral_allele
    - evidence
    - clinical_significance
    - global minor allele, frequency and count
Incl_consequences files include sift (if available for this species)
and polyphen (human only) predictions.


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

We use the sum command for calculating checksums.

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

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Example content from the human germline VCF dump is shown below:

##fileformat=VCFv4.1
##fileDate=20140713
##source=ensembl;version=76;url=http://e76.ensembl.org/Gallus_gallus
##reference=ftp://ftp.ensembl.org/pub/release-76/fasta/Gallus_gallus/dna/
##INFO=<ID=dbSNP_140,Number=0,Type=Flag,Description="Variants (including SNPs and indels) imported from dbSNP">
##INFO=<ID=TSA,Number=1,Type=String,Description="Type of sequence alteration. Child of term sequence_alteration as defined by the sequence ontology project.">
##INFO=<ID=E_Cited,Number=0,Type=Flag,Description="Cited.http://www.ensembl.org/info/docs/variation/data_description.html#evidence_status">
##INFO=<ID=E_ESP,Number=0,Type=Flag,Description="ESP.http://www.ensembl.org/info/docs/variation/data_description.html#evidence_status">
##INFO=<ID=E_1000G,Number=0,Type=Flag,Description="1000Genomes.http://www.ensembl.org/info/docs/variation/data_description.html#evidence_status">
##INFO=<ID=E_Multiple_observations,Number=0,Type=Flag,Description="Multiple_observations.http://www.ensembl.org/info/docs/variation/data_description.html#evidence_status">
##INFO=<ID=E_Freq,Number=0,Type=Flag,Description="Frequency.http://www.ensembl.org/info/docs/variation/data_description.html#evidence_status">
##INFO=<ID=E_Hapmap,Number=0,Type=Flag,Description="HapMap.http://www.ensembl.org/info/docs/variation/data_description.html#evidence_status">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
1       1819    rs14807616      G       T       .       .       dbSNP_140;TSA=SNV;E_Freq
1       1830    rs14807617      G       A       .       .       dbSNP_140;TSA=SNV;E_Freq
1       1878    rs14222596      G       C       .       .       dbSNP_140;TSA=SNV;E_Freq
1       1907    rs13935659      G       T       .       .       dbSNP_140;TSA=SNV;E_Freq
1       1916    rs13789020      C       T       .       .       dbSNP_140;TSA=SNV;E_Freq
1       1920    rs14354723      C       T       .       .       dbSNP_140;TSA=SNV;E_Freq
1       1921    rs15416557      A       G       .       .       dbSNP_140;TSA=SNV;E_Freq
1       2187    rs318013082     C       G       .       .       dbSNP_140;TSA=SNV
1       2311    rs14723176      G       A       .       .       dbSNP_140;TSA=SNV;E_Freq
1       2350    rs14707527      T       C       .       .       dbSNP_140;TSA=SNV;E_Freq
1       3664    rs13813940      A       T       .       .       dbSNP_140;TSA=SNV;E_Multiple_observations;E_Freq
1       3668    rs314311150     C       A       .       .       dbSNP_140;TSA=SNV
1       4170    rs16708515      T       C       .       .       dbSNP_140;TSA=SNV;E_Freq
1       4672    rs16753437      A       G       .       .       dbSNP_140;TSA=SNV;E_Freq
1       8512    rs16753440      C       T       .       .       dbSNP_140;TSA=SNV;E_Freq
1       8552    rs16753441      C       T       .       .       dbSNP_140;TSA=SNV;E_Freq
1       8610    rs14743337      A       G       .       .       dbSNP_140;TSA=SNV;E_Freq


