This directory contains the 20120430.sample_summary_with_status.txt which is a tab delimited
file that describes the current summary of each sample for both exome and low coverage sequencing 
from the DCC perspective.

All its alignment data is based on the 20111114 alignment release. 
The genome size considered is 2750000000.

This file contains the columns

Sample
Population      
Phase   Is the same part of phase 1 or 2
Low Coverage Center     
LC Meta Data Present    Meta Data is present in the ENA database for this sample at low coverage
BP in ENA       The Number of basepairs at the ENA for this sample at low coverage
BP at DCC       The Number of basepairs at the DCC for this sample at low coverage
Total Bases Aligned     The number of input bases to the 20111114 low coverage alignment
Raw Aligned Coverage    The x coverage for all aligned bases
Coverage at Omni sites  The non duplicated x coverage at omni sites
Non Dup Coverage        The total non duplicated coverage across the Genomes
Exome Center    
Exome Meta Data Present 
BP at ENA       
BP at DCC       
Total Aligned   
Percent of Targets >20x The percentage of targets covered to > 20X as calculated by CalculateHsMetrics from Picard
LC Complete     Completion status for the Low coverage sequence (> 2.7 x non dup coverage is complete)
Exome Complete  Completion status for exome sequence (> 0.7 percent of targets coverage > 20x is complete)
LC Alignment    Has an alignment
E Alignment     
Failed Genotype QC      Failed sequence level genotype qc
Failed Short Indel QC   Failed the overrepresentation of short indels qc
Failed VerifyBamID      Failed the VerifyBamID qc
LC Sufficent Raw        Has sufficient raw low coverage data (If the sample is not already complete this means either there is no alignment and more than 10GB of raw 
sequence of there is an alignment and at least 2.75GB of new sequence is avaialble since the last alignment was run)
Exome Sufficient Raw    Has sufficient raw exome data (If the sample is not already complete this means either there is no alignment and at least 1GB of raw sequence or 
there is an alignment and at least 500MB of new sequence is available since the last alignment was run)

The 3 QC processes that were run are:

Genotype QC, This is a pre alignment qc process run for each run_id, The run is subsampled,
             aligned to the reference and then genotypes called and compared to know genotypes from
             the omni platform

Short Indel QC, This is a process which checks for overrepresentation of short indels which may
                indicate an error in the sequence process. This check was designed by Li Heng 
                and the c script can be found in the center_summaries directory

VerifyBamID, This is a test from Hyun Min Kang UMich http://genome.sph.umich.edu/wiki/VerifyBamID
             It is run on the completed alignment files. It checks sample identity like the Genotype 
             QC test. It also checks other metrics like number of heterozygous sites and number of
             hom alt sites. The measures provide a likelihood that the sequence is contaminated rather
             than a sample swap

A breakdown of the runs which fail these checks for each sample can be found in the center_summaries
directory