Benchmarking
See how your variant calling stacks up
Wondering how your variant calling workflow is performing? Upload your HG002 VCF to see how it compares.
See Sample ReportGet VCF
Generate or find an HG002 VCF file or proceed to step 2 to get started with a provided VCF file
Upload/Select VCF
Upload your HG002 VCF or select one from the list of provided VCF files
Run
Hit run to start the workflow
View Results
Get notified when the job is complete and view reports right in your browser
Compare
Navigate to the Performance Metrics table to compare benchmarking metrics across your submissions
This workflow benchmarks your submitted GRCh38 HG002 VCF with the Genome in a Bottle v4.2.1 truth set from NIST for the high confidence regions, MHC, and difficult to map regions. Results of the benchmark then compared to benchmarks from the winners of the PrecisionFDA v2 challenge.
Get Data
Fastqs
Get HG002 fastq files from Illumina, PacBio, and ONT sequencers.
| NIST | https://data.nist.gov/od/id/mds2-2336 |
|---|---|
| GIAB S3 (Must be signed into AWS console) | https://s3.console.aws.amazon.com/s3/buckets/giab?region=us-east-1&prefix=data/AshkenazimTrio/HG002_NA24385_son/ |
VCFs
Want to find existing HG002 VCF files to submit? Check out these publicly available locations
| NIST | https://data.nist.gov/od/id/mds2-2336 |
|---|---|
| https://datasetsearch.research.google.com/search?query=hg002&docid=L2cvMTFwdHRfbms0dA%3D%3D |