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Figure 1 | Genome Medicine

Figure 1

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

Figure 1

Mean single-nucleotide variants (SNV) concordance over 15 exomes between five alignment and variant-calling pipelines. The alignment method used, followed by the SNV variant calling algorithm is annotated here in shorthand: BWA-GATK, SOAP-Align-SOAPsnp, BWA-SNVer, BWA-SAMtools, and GNUMAP-GNUMAP. (A) Mean SNV concordance between each pipeline was determined by matching the genomic coordinate as well as the base-pair change and zygosity for each detected SNV. (B) The same analysis as in (A) but filtered to include only SNVs already found in dbSNP135. (C) The same analysis as in (A), but filtered to include novel SNVs (that is, SNVs not found in dbSNP135).

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Genome Medicine

ISSN: 1756-994X

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