Are special read alignment strategies necessary and cost-effective when handling sequencing reads from patient-derived tumor xenografts?

Table 2 False non-synonymous SNVs called by the different strategies, with reads generated from both exonic and non-exonic regions

Strategy	False positive non-synonymous SNVs	False negative non-synonymous SNVs
No contamination	0	228
Direct	47	251
Filtering	0	265
Combined	3	70

False non-synonymous SNVs called by the different strategies, and true non-synonymous SNVs missed by them, under the mH.len100.eL setting with 1:1 human-mouse mixing ratio and reads generated from both exonic and non-exonic regions of human chromosome 14 and mouse chromosome 12.