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Figure 2 | Genome Medicine

Figure 2

From: Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

Figure 2

Single-nucleotide variant (SNV) concordance, between two sequencing pipelines (Illumina and Complete Genomics (CG)) for a single exome, k8101-49685. For the Illumina sequencing, exons were captured using the Agilent SureSelect version 2 panel of capture probes. CG SNVs consisted of a subset of all SNVs called by CG that fell within the Agilent SureSelect version 2 exons. Concordance was determined by matching the genomic coordinates, base-pair composition, and zygosity status for each detected SNVs. Illumina SNVs consisted of all SNVs (the union) called by the five variant-calling pipelines GATK, SAMtools, SOAPsnp, SNVer, and GNUMAP, which increased the false positives but decreased the false negatives. Concordance was measured between Illumina SNVs and (A) all CG SNVs, (C) only high-quality (VQHIGH) CG SNVs, and (D) only low quality (VQLOW) CG SNVs. (B) Genome mappability analyses were performed on 2,085 discordant SNVs, which were found by the CG pipeline and not found by any of the five Illumina data pipelines.

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Genome Medicine

ISSN: 1756-994X

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