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Figure 4 | Genome Medicine

Figure 4

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

Figure 4

Indel concordance for a single exome, k8101-49685, between two sequencing pipelines: Illumina and Complete Genomics (CG). Illumina indels consist of a union of all indels called by each of the three indel-calling pipelines GATK, SOAPindel, and SAMtools. CG indels consisted of a subset of indels called by CG that fell within the Agilent SureSelect version 2 exons. Both Illumina and CG indels were left normalized and intervalized to a range of 20 genomic coordinates (10 coordinates on each side of the normalized position). To determine whether or not indels were matching, the genomic coordinates as well as the base length and composition of each indel were considered.

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Genome Medicine

ISSN: 1756-994X

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