This document describes the known issues with this call set which
the consortium are working on fixing.

If an issue has a Fixed tag, this gives the date and the version which
has been fixed, any future files should also contain the fix.

The version associated with last update was the first version the
issue was discovered.

Please be aware that the consortium is still reviewing this data and a
number of known issues have been identified. The callset should therefore not be
considered final and is subject to change in the near future.

Related individuals have been included in the candidate release callset.
These individuals will be removed to a separate VCF prior to formal release.
Last update: 20140626 v1
Fixed : 20140804 v3

A number of bi-allelic large deletions have been left out of this dataset
and will be added back in.
Last update: 20140626 v1
Fixed: 20140708, v2

The candidate release has filtered common variants in a overly harsh manner.
As such, a number of variants appear to be lost in comparison to Phase 1.
The majority of these variants will be added back to the callset in
the near future.
Last update: 20140626 v1
Fixed: 20140804 v3

Structural variants need to be consolidated across variant types.
Last update: 20140626 v1
Fixed 20140804 v3

This release has been annotated by functional consequence.
Last update: 20140626 v1
Fixed 20140910 v5 found in ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/functional_annotation/

This release has not yet been annotated with ancestral alleles.
Last update: 20140626 v1
Fixed 20140910 v5 found in ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/functional_annotation/

The release candidate does not include chromosomes X or Y.
Last update: 20141018 v5, Chromosome X had been added, we hope to add chrY soon

Super population Allele Frequences and Total Depth have been added to the info column
Last update 20140626 v1
Fixed 20140910 v5 these are described in ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/release/20130502/README_vcf_info_annotation.20140910

Release v3 is still missing biallelic snvs from chr12:7000000-10000000
Last update 20140804 v3
Fixed update 20140821 v4

Release v4 does not have the genotypes for the 31 related invididuals
Last update 20140820 v4
Fixed update 20140910 v5 These are now found in ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/release/20130502/

The release files upto v4 contain 4213 sites for which some individuals whose genotypes had missing values. 
Last update 20140820 v4
Fixed 20140910 v5 These rows wer filtered out

chrX data were added to the release directory without the standard annotation (sub-continental super population allele frequency, depth and ancestral alleles);
functional annotation is not ready either for chrX.
Last update 20141017 v5
Fixed 20141030 annotations for chrX are added to the VCF file

The super-population level allele frequency is over-estimated for chrX and chrY 
Last update 20141017 v5
Fixed 20150813 chrX and chrY genotype VCF files v1b version, the whole genome site VCF file v5b version now have correct super-population AF