Author: Edico Genome Bioinformatics Team
PrecisionFDA’s most recent challenge, Hidden Treasures – Warm Up, challenged participants to investigate the accuracy of their pipelines by testing the ability to find in silico injected variants in FASTQ files from exome sequencing of reference cell lines.
At Festival of Genomics Boston on Oct. 4, 2017, PrecisionFDA announced the results of its latest challenge, of which there were 86 valid entries from 30 participants. Out of the 86 entries, 45 found all 50 injected variants. Among entries catching all 50 injected variants, Edico Genome’s DRAGEN V2 Germline Pipeline received the highest score in five of the six accuracy metrics: SNP recall and SNP F-score, and indel precision, indel recall and indel F-score, and placed second on the sixth metric (SNP precision). Through all aspects of the challenge, DRAGEN emerged as a top player, receiving Warm Up in silico Variant Catchers and Warm Up in silico VAF Spotters badges on most submissions.
DRAGEN V2 is the second iteration of the DRAGEN Germline Pipeline, which employs improved sample-specific calibration of the sequencer and sample prep error models, as well as an improved mapper and aligner algorithm. The same fundamental improvements are also applicable to DRAGEN’s Somatic Pipeline.
For a list of full results, visit: https://precision.fda.gov/challenges/1/view/results