This readme explains in more detail what experimental validation data is available
for this release.

The experimental validation data can be found in experimental_validation
directories like this

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/working/20100618_pilot_paper_data/low_coverage/snps/experimental_validation

low_coverage
------------

snps:

The low coverage snps were validated using a Sequenom assay. The files available
are:

low_coverage.2009_10.snps_and_indel_validation_chr20:

These files contains two sets of SNPs. First a randomly selected set of novel SNPs 
from chr20. Second a set of snps with functional consequences (Loss of Function or 
Non Synonymous) or with large differences in allele frequencies between 2 of the 3 
populations.  

low_coverage.2010_07.1KG_100K_snp_chip:

indels:

low_coverage.2010_07.indel_validation:

Some of the low coverage indels were validated alongside the chromosome 20 snps and
can be found in the file descirbed above but an additional round of indel validation 
was carried out other chromosome 20 indels and the results are in these files.

trio
----

snps

Sequenom assays of trio snps was done in late 2008 and early 2009

trio.2009_12.batch1_2_validation
trio.2009_12.batch5_validation
trio.2009_12.batch6_validation

exon
----

snps

Both Sequenom and Targetted Capillary sequencing was used to validate the SNPs
discovered in the exon targetted sequencing.

The Sequenom assays included randomly selected snps, snps discovered in a particular
population, low frequency snps and some singletons.

exon.2010_07.sequenom_series1_random
CEU.exon.2010_07.sequenom_series2
CHB.exon.2010_07_sequenom_series2
YRI.exon.2010_07_sequenom_series2
exon.2010_07.sequenom_series4_low_freq
exon.2010_07.sequenom_series4_singletons

The targetted capillary sequencing was used to validate low frequency and
functionally important variants

exon.2010_07.targetted_cap_series3_low_freq
exon.2010_07.targetted_cap_series5_functional