TY  - JOUR
A1  - Ajay, Subramanian S.
A1  - Parker, Stephen C.J.
A1  - Ozel Abaan, Hatice
A1  - Fuentes Fajardo, Karin V.
A1  - Margulies, Elliott H.
T1  - Accurate and comprehensive sequencing of personal genomes
Y1  - 2011/09/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1498 
EP  - 1505 
DO  - 10.1101/gr.123638.111 
VL  - 21 
IS  - 9 
UR  - http://genome.cshlp.org/content/21/9/1498.abstract 
N2  - As whole-genome sequencing becomes commoditized and we begin to sequence and analyze personal genomes for clinical and diagnostic purposes, it is necessary to understand what constitutes a complete sequencing experiment for determining genotypes and detecting single-nucleotide variants. Here, we show that the current recommendation of ∼30× coverage is not adequate to produce genotype calls across a large fraction of the genome with acceptably low error rates. Our results are based on analyses of a clinical sample sequenced on two related Illumina platforms, GAIIx and HiSeq 2000, to a very high depth (126×). We used these data to establish genotype-calling filters that dramatically increase accuracy. We also empirically determined how the callable portion of the genome varies as a function of the amount of sequence data used. These results help provide a “sequencing guide” for future whole-genome sequencing decisions and metrics by which coverage statistics should be reported. 
ER  -