The "All" group thus contains samples with merged QC pass lanes, samples with merged QC fail lanes, and samples with merged QC pass and QC fail lanes.
Samples lacking two replicate lanes in either the QC pass or QC fail group were excluded from this analysis.
For the reproducibility comparison (Additional file 1), Pearson r was calculated using 2 replicate lanes corresponding to each sample represented in the QC pass and QC fail groups.
> -wrap-foot> Calls from Illuminus and GenoSNP produce the most discordant results at QC (with 5157 and 8815 unique QC passes and fails, respectively) whereas GenCall and optiCall appear to have more overlapping QC outcomes with other callers.
To assess clustering quality and accuracy, 600 unique QC pass SNPs and 600 unique QC fail SNPs were selected at random and manually called using a modified version of Evoker (Morris et al., 2010).
The percentage of total reads that passed quality control as described in Materials and Methods (% QC Passed) and the number (Mapped Reads) and percentage of reads that were successfully mapped to the mouse genome (% Mapped) are shown.
Pearson's correlation was calculated for all pairwise comparisons (i.e., 24 × 24 comparison of samples both passing QC, 24 × 10 among samples passing QC and samples failing QC, and 10 × 10 comparison of samples both failing QC).
Coefficient of variation analysis was used to determine variability in expression levels for each of the 100 maintenance genes across the 10 samples failing QC criteria and across 10 samples passing QC criteria.
If QC is passed, the primary hits are selected for a second round of screening.
In the example given above, as the coverage of 1X, 4X, 10X and 20X supporting reads decreases slowly, this QC is passed.
