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Table 2 Comparison of the analytic performance of a conventional alignment and variant calling pipeline (GSNAP with GATK minus VQSR), with a novel, extremely rapid method (DRAGEN)

From: A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases

Sample SBS18 yield (GB) Site Pipeline Reads aligned Alignments with mapping quality >20 Variants called Mismatch rate Indel rate % Paired Reads Strand balance % Chimeric Reads Rare, potentially pathogenic variants Analytic sensitivity (GeT-RM or SNP array) Analytic specificity (GeT-RM or SNP array) Analytic sensitivity (full GIAB) Analytic specificity (full GIAB)
NA12878 133 Essex DRAGEN 99.4 % 95.48 % 4,782,970 0.0029 0.00017 99.55 % 0.500 0.69 % 658 99.93 % 99.87 % 99.69 % 99.99 %
GSNAP/GATK-1.6/noVQSR 98.5 % 96.33 % 5,343,988 0.0056 0.00017 98.55 % 0.496 0.82 % 783 99.54 % 98.57 % 98.21 % 99.99 %
NA12878 65a CMH DRAGEN 97.7 % 91.31 % 4,633,357 0.0060 0.00023 99.18 % 0.501 1.89 % 775 99.42 % 99.46 % 98.63 % 99.99 %
GSNAP/GATK-3.2/noVQSR 96.2 % 92.86 % 4,571,157 0.0079 0.00021 97.55 % 0.499 1.75 % 593 97.29 % 95.35 % 95.74 % 99.99 %
UDT_173 106 Essex DRAGEN 99.5 % 94.92 % 4,742,150 0.0034 0.00020 99.80 % 0.500 1.12 % 620 96.13 % 97.74 % n.a. n.a.
GSNAP/GATK-1.6/noVQSR 99.3 % 96.88 % 4,294,504 0.0034 0.00019 99.34 % 0.500 0.90 % 512 88.54 % 98.06 % n.a. n.a.
  1. All runs were 18-h WGS. The NA12878 reference genotypes were NIST High Confidence calls from GeT-RM/NA12878.NIST-GIAB_v.2.18 (labeled ‘GeT-RM’) or the full GIAB dataset (labeled ‘full GIAB’). UDT_173 were results of hybridization to the Omni4 SNP array. GSNAP was version 2012.07.12, with default parameters, and GATK was version 1.6.13 or 3.2, without VQSR. DRAGEN was version 1.2. % paired, percentage of reads whose mate was also aligned; Strand balance, reads aligned to the forward strand divided by total reads aligned; % chimeric, percentage of chimeric alignments (mates >100 kb apart or on different chromosomes). aSingle flowcell