5-base Small Variants

Currently, Illumina 5-base supports only PCR prep The DRAGEN Germline Small Variant Caller takes mapped and aligned DNA reads as input and calls SNPs and indels through a combination of column-wise detection and local de novo assembly of haplotypes. For more information, refer to the DRAGEN user guide.

HG002 performance

DRAGEN: 4.5.4 | Truthset: GIAB/NIST high-confidence | Reference: GRCh38

HG002 NIST small variants summary (click to expand)

Variant	Recall	Precision	F1-score	FN	FP	FP+FN
SNP	0.998561	0.999357	0.998959	4848	2164	7012
INDEL	0.982097	0.990685	0.986372	9357	4826	14183

HG002 NIST FP+FN summary

T2TQ100-v1.1-v0.019

DRAGEN: 4.5.4 | Truthset: T2TQ100-v1.1-v0.019 | Reference: GRCh38

HG002 T2TQ100-v1.1-v0.019 small variants summary (click to expand)

Variant	Recall	Precision	F1-score	FN	FP	FP+FN
SNP	0.99155	0.996665	0.994101	30872	12124	42996
INDEL	0.892639	0.992973	0.940137	56919	5462	62381

HG002 T2TQ100-v1.1-v0.019 FP+FN summary