Figure 1

Variant calling procedure in the Exon Pilot Project. (a) The SNP calling procedure. Read alignment and SNP calling were carried out by Boston College (BC) and the Broad Institute (BI) independently using complementary pipelines. The call sets were intersected for the final release. (b) The INDEL calling procedure. INDELs were called on the Illumina and Roche 454 platforms. The sequence was processed on three independent pipelines, Illumina at the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC), Illumina at BI, and Roche 454 at BCM-HGSC. The union of the three call sets formed the final call set. The Venn diagram provided is not to scale. AB: allele balance; MSA: multiple sequence alignment; QDP: discovery confidence of the variant divided by the depth of coverage; SW: software.