Data Setup

To help get started quickly, we have pre-processed some of the public domain data (more specifically, the data and truth sets shared during the Precision FDA Truth challenge) and made them available for instant use. They can be downloaded from our public S3 bucket links mentioned below.

Common

hs37d5 reference

https://dl4vc.s3.us-east-2.amazonaws.com/hs37d5.fa

https://dl4vc.s3.us-east-2.amazonaws.com/hs37d5.fa.fai

Training

HG001 50x BAM (generated from precisionFDA HG001 FASTQ file)

https://dl4vc.s3.us-east-2.amazonaws.com/HG001-NA12878-50x.sort.bam

https://dl4vc.s3.us-east-2.amazonaws.com/HG001-NA12878-50x.sort.bam.bai

Truth set split by multi-allele and normalized

https://dl4vc.s3.us-east-2.amazonaws.com/NA12878_GIAB_highconf_IllFB-IllGATKHC-CG-Ion-Solid_ALLCHROM_v3.2.2_highconf.bcf

https://dl4vc.s3.us-east-2.amazonaws.com/NA12878_GIAB_highconf_IllFB-IllGATKHC-CG-Ion-Solid_ALLCHROM_v3.2.2_highconf.bcf.csi

High confidence region

https://dl4vc.s3.us-east-2.amazonaws.com/NA12878_GIAB_highconf_IllFB-IllGATKHC-CG-Ion-Solid_ALLCHROM_v3.2.2_highconf.bed

Evaluation

HG002 50x BAM (generated from pFGA HG002 FASTQ file)

https://dl4vc.s3.us-east-2.amazonaws.com/HG002-NA24385-50x.sort.bam

https://dl4vc.s3.us-east-2.amazonaws.com/HG002-NA24385-50x.sort.bam.bai

Truth set split by multi-allele and normalized

https://dl4vc.s3.us-east-2.amazonaws.com/HG002_GIAB_highconf_IllFB-IllGATKHC-CG-Ion-Solid_CHROM1-22_v3.2.2_highconf.bcf

https://dl4vc.s3.us-east-2.amazonaws.com/NA12878_GIAB_highconf_IllFB-IllGATKHC-CG-Ion-Solid_ALLCHROM_v3.2.2_highconf.bcf.csi

High confidence region

https://dl4vc.s3.us-east-2.amazonaws.com/HG002_GIAB_highconf_IllFB-IllGATKHC-CG-Ion-Solid_CHROM1-22_v3.2.2_highconf.bed

High recall variant candidates in ihgh confidence region

https://dl4vc.s3.us-east-2.amazonaws.com/HG002-NA24385-50x-candidates.vcf.gz

https://dl4vc.s3.us-east-2.amazonaws.com/HG002-NA24385-50x-candidates.vcf.gz.csi