Fig. 2: Variant calling process used in prevalence study. | Genetics in Medicine

Fig. 2: Variant calling process used in prevalence study.

From: One in seven pathogenic variants can be challenging to detect by NGS: an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation

Fig. 2

A next-generation sequencing (NGS) workflow designed to detect a wide variety of variant types was used in our prevalence study, sensitivity study, and also our pilot study (workflow 1B). NGS reads are aligned to a modified reference genome and multiple variant callers are then applied. Follow-up assays are used to confirm potential false positives, to determine the exact sequence of complex variants, and to resolve the location of variants within segmental duplications. For details see “Materials and Methods.” CNVs copy-number variants, GATK Genome Analysis Toolkit, Indels insertions or deletions, LR-PCR long-range polymerase chain reaction, MEIs mobile element insertions, NGS next-generation sequencing, QC quality control, Segdup segmental duplication, SNVs single-nucleotide variants.

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