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Figure 5 | Genome Medicine

Figure 5

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

Figure 5

MiSeq validation experiment on a subset of Illumina-data calls. A total of 1,140 SNVs from sample k8101-49685 were randomly sampled for MiSeq validation, with 380 sampled from the set of unique-to-GATK SNVs, 380 sampled from the set of unique-to-SOAPsnp SNVs, and 380 sampled from the set that were overlapping between these two pipelines. There were 919 (81.0%) of these variants that were successfully amplified and sequenced. BWA version 0.6.2 and GATK version 2.3-9 were used to process the sequencing data for variant-calling. Additionally, 960 indels from sample k8101-49685 were randomly selected for validation. Of these, 386 were randomly selected from the unique-to-GATK indel set, 387 were randomly selected from the unique-to-SOAPindel set, and 187 were randomly selected from the set of indels overlapping between the two (SOAPindel and GATK). There were 841 (83.5%)of these indels that were successfully amplified and sequenced. BWA version 0.6.2 and GATK version 2.3-9 were used to determine the number of variants that were also successfully validated across these sets.

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