Table 1.

Exome-seq datasets summary.

	EC (Exome-seq)	OC (Exome-seq, WUGSC)	OC (Exome-seq, BI)
No. of samples	248	79	136
Sequencing technology	Illumina GAIIx or Hiseq. 2000	Illumina GAIIx or ABI 3730	Illumina GAIIx
Coverage per sample	at least 20x	at least 20x	at least 20x
Read architecture	100 bp paired end	100 bp paired end	76 bp paired end
Target area	whole exome	whole exome	whole exome
Data set source	TCGA Research Network	TCGA Research Network	TCGA Research Network
Aligner	BWA	BWA	Picard
	BC (Exome-seq)	Cutaneous Melanoma (Exome-seq)
No. of samples	503	342
Sequencing technology	Illumina Hiseq. 2000	Illumina HiSeq. 2000
Coverage per sample	~20x	~82x
Read architecture	100 bp paired end	76 bp paired end
Target area	whole exome	whole exome
Data set source	TCGA Research Network	TCGA Research Network
Aligner	BWA	BWA/Picard