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 Report
Get VCF
Get VCF
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Generate or find an HG002 VCF file or proceed to step 2 to get started with a provided VCF file

Upload/Select VCF
Upload/Select VCF
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Upload your HG002 VCF or select one from the list of provided VCF files

Run
Run
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Hit run to start the workflow

View Results
View Results
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Get notified when the job is complete and view reports right in your browser

Compare
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.

NISThttps://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

NISThttps://data.nist.gov/od/id/mds2-2336
Googlehttps://datasetsearch.research.google.com/search?query=hg002&docid=L2cvMTFwdHRfbms0dA%3D%3D

Access these additional features as a subscriber

1

Select additional regions of interest

2

Use different subjects and truth sets

3

Choose different genome references

4

Specify other VCF files to compare against