Table 1.
Variant calling software tools.
Table 2.
Classification of germline and somatic events.
Table 3.
Post-processing checks performed by qSNP.
Table 4.
Details of verification using amplicon-based sequencing on the Ion Torrent.
Figure 1.
Non-independent reads confounding mutation calls.
Read pairs are colored by the chromosome map position of the second read in the pair. MarkDuplicates fails to correctly identify these non-independent read pairs as PCR duplicates due to the different map locations of the second read.
Table 5.
Controlled mixture experiment to assess the effect of reducing tumor purity on somatic mutation detection using the SOLiD v4 platform.
Figure 2.
Overlap in somatic mutation calls.
Verified somatic mutation calls were compared across three callers in 5 different tumor purity mixtures. Values are number of calls in 100%, 80%, 60%, 40% and 20% tumor content mixture, from top to bottom.
Table 6.
Controlled mixture experiment to assess the effect of reducing tumor purity on somatic mutation detection using the HiSeq2000 platform.
Table 7.
Benchmarking qSNP on sequencing data from the SOLiD v4 and HiSeq 2000 platforms using COLO-829 variants verified by either WTSI (WTSI only, qSNP+WTSI) or QCMG (qSNP only).