This release contains snp calls based on data from all 3 pilot studies.

This directory also contains 2010_03_release.md5s.
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_03_release.md5s
This is a list of the md5sum for each file which is part of the release.

All the vcf files are named using a standard convention

POP.SRP0000XX.2010_03.vcf.gz

In this naming schema POP represents the populations including in that data set.
The SRP represents the study id associated with the data set. The date is the
release date.
 
There are 3 directories

pilot1 contains data for the pilot1 (SRP000031) release.
There should be 6 vcf files, two each  for CEU, YRI and CHB+JPT.

Files named similar to: POP.SRP000031.2010_03.genotypes.vcf.gz 
contain snp calls with genotype information included.

Files named similar to: POP.SRP000031.2010_03.sites.vcf.gz 
contain snp calls without genotype information included.

This convention is applies to the pilot 2 and pilot3 vcf files.


pilot2 contains data for the pilot2 (SRP000032) release. 
Here there are 2 vcf files, 4 for each of the trios.


pilot3 contains data for the pilot3 (SRP000033) release. 
Here there are 14 vcf files, two for each of the populations sampled for pilot3.


Each of the above vcf files is accompanied by a .tbi file. This is 
a 'tabix' index file for faster access to selective regions of the vcf file.
See:
http://sourceforge.net/projects/samtools/files/
for download 

also
http://samtools.sourceforge.net/tabix.shtml
for manual page.


Each directory also contains both a sequence.index file and an alignment.index
file. They are named in the form 2010_02.SRP0000XX.nnnnn.index.

These index files follow the formats as described in these readmes

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/README.sequence.index
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/README.alignment.index

These snp calls represent merged data sets from different groups.

The Sanger Insitute, the Broad Insititute and The University of Michigan contributed to the pilot1 snp calls.
The Broad and the University of Michigan contributed to the pilot2 snp calls.
The Broad and Boston College contributed to the pilot3 snp calls.

The initial call sets which contributed to these sets can be found in 
pilotX/supporting 


The pilot1 sequenom validation data can be found in
pilot1/experimental_validation


The pilot3 sequenom validation data can be found in
pilot3/experimental_validation

Pilot 1 indels can be found in 
pilot1/indels