Table 2.

Mutations missed by standard WES pipeline and mechanism.

Sanger call	WES call	Ref/Alt	Genotype quality (> 20)	Quality By Depth (> 2)	Mapping quality (> 40)	Fisher strand	Nature of failure
c.925G > A (p.Gly309Arg)	chr17:78081665G > A	4/3	72.74	8.74	60	0	Missense, filtered out
c.925G > A (p.Gly309Arg)	Not called out by GATK	10/2	–	–	–	–	Missense, not called
c.-32-17_-32-10delins30	chr17:g.78078341T > C	9/3	99	4.05	54.44	0	Insertion not called. VQSLOD 3.26
c.1195-19_2190-17del (p.Asp399fs*6) 8273 bp deletion in intron7-exon15 seen in Hispanic population	Not called out by GATK UnifiedGenotyper	–	–	–	–	–	Very large deletion
c.2481 + 102_2646 + 31del common 537 bp deletion from intron17-intron18	Not called out by GATK UnifiedGenotyper	–	–	–	–	–	Large deletion
c.148_859del exons 2–4	Not called out by GATK UnifiedGenotyper	–	–	–	–	–	Large deletion
Exons 15–20 deletion breakpoint not localized	Not called out by GATK UnifiedGenotyper	–	–	–	–	–	Very large deletion