Finding a suitable library size to call variants in RNA-Seq

BMC Bioinformatics

Table 1 Types of variants in the Leucegene truth sets

Mutation type	Min VAF	Mean VAF	Max VAF	N
Composite indel	0.06	0.25	0.56	9
Long insertion	0.41	0.5	0.64	3
Short deletion	0.09	0.24	0.38	2
Short insertion	0.07	0.33	0.84	15
SNVs	0.05	0.37	0.97	58
Indel-not reported	0.84	0.84	0.84	1

Variants used as the truth set were previously validated in a set of 45 CBF-AML RNA-Seq samples [9]. Variant types are inferred from the information in the published study and by the variant calls performed on the initial samples. A short indel (insertion/deletion) is an indel < 10 bp long; composite indels are mutations including both inserted and deleted nucleotides; SNVs are single nucleotide variants

ISSN: 1471-2105