Skip to main content
Fig. 1 | BMC Medical Genomics

Fig. 1

From: Identification of single nucleotide variants using position-specific error estimation in deep sequencing data

Fig. 1

Graphical representation of AmpliSolve’s workflow for estimating the noise levels and detecting SNVs. The workflow comprises the following steps: a Screening the available normal samples to identify reads supporting alleles other than the reference. b Error estimation per position, per nucleotide and per strand for all positions in the gene panel based on the distribution of alternative allele counts in (a); only alternative counts corresponding to VAF < 5% are taken into consideration; c For each genomic position in a tumor sample, the method identifies the total coverage of the position and the number of reads supporting the alternative alleles, if any. d Given the information from steps b and c the method applies a Poisson distribution-based model to compute the p-value that the variant (red line) is real. This p-value is then transformed to a quality score that is used by AmpliSolve together with additional quality criteria to identify SNVs

Back to article page