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