• Variant Annotation Table (VAT)

Variant-level metadata and functional annotations for  the SNP and Indel variants contained in the srWGS data.

Please see Variant Annotation Table for more details, including the provided fields.

• Ancestry information

…/ancestry/ancestry_preds.tsv

…/ancestry/preds_oth.html

…/ancestry/merged_sites_only_intersection.vcf.bgz

…/ancestry/merged_sites_only_intersection.vcf.bgz.tbi

…/ancestry/loadings.ht

Computed ancestry predictions for all samples in the srWGS joint callset (tsv).  We also provide a plot of the ancestry predictions and the sites-only VCF (vcf.bgz) of the locations we used for training the ancestry classifier. Furthermore, we supply the coefficients of PCs utilized by the ancestry predictions classifier.

Please see Genetic predicted ancestry for more information on these files.

For more information on how we predict ancestry, please see the All Of Us Release Genomic Quality Report (Appendix A)

• QC information

…/qc/flagged_samples.tsv

…/qc/metrics.html

…/qc/pc1vspc2.html

…/qc/genomic_metrics.tsv

The list of srWGS samples flagged in the joint callset QC process (tsv) and metrics related to the genomic sequencing of the WGS samples.  We also include plots of the metric residuals and the first two principal components (*.html) used in the Ancestry and Joint Callset QC.

Please see Flagged srWGS Samples for details on the tsv format.

Please see the All Of Us Release Genomic Quality Report (Joint Callset QC) for details on how we flag samples.

One srWGS sample (person_id: 3518297) does not have its corresponding array in the array Hail MT and PLINK files.  Please note that the array VCF for this sample will be available.  For more information, please see All Of Us Release Genomic Quality Report (Known Issue #4)

• Relatedness

…/relatedness/relatedness.tsv

…/relatedness/relatedness_flagged_samples.tsv

The relatedness of the srWGS samples as kinship scores.  We provide one file which lists all pairs of samples w/ a kinship score greater than 0.1 (relatedness.tsv).  We also provide a list of samples that would need to be removed to remove related samples from the full cohort.  (relatedness_flagged_samples.tsv)

Please see Relatedness for more information.

These subset files include srWGS SNP and Indel variants that are within exon regions of the Gencode v42 basic transcripts, for all samples. The exome srWGS callset is provided in VCF, Hail MT, BGEN, and PLINK bed formats.

For more information on how we determine the exome, please see Smaller callsets for analyzing srWGS SNP & Indel data with Hail MT, VCF, and PLINK.

Note: The exome smaller callsets were updated on 9/22/23 with an update to all three smaller callsets; more details can be found in this article. The new versions are referred to as version 7.1.

• Hail MT

gs://fc-aou-datasets-controlled/v7/wgs/short_read/snpindel/exome_v7.1/multiMT/hail.mt

Hail multiallelic MatrixTable (MT) for the exome srWGS joint callset. Multiallelic sites are not split.

When using this file in Hail, read directly from the bucket location.  Do not attempt to copy it locally. Please see srWGS SNP & Indel Hail MT for more information.

• VCF

Variant Call Format (VCF) for the exome srWGS joint callset.  This callset is converted from the exome Hail MT and sharded by chromosome into multiple files. 

Please see srWGS SNP & Indel VCFs for more information

• Hail MT multiallelic split

• PLINK BED

• BGEN

• UCSC BED

These subset files include srWGS SNP and Indel variants that are frequent in the All of Us computed ancestry subpopulations. We use population-specific allele frequency (AF) > 1% or population-specific allele count (AC) > 100, in any computed ancestry subpopulations. The ACAF threshold srWGS callset is provided in VCF, Hail MT, BGEN, and PLINK bed formats.

For more information on these subset files, please see Smaller callsets for analyzing srWGS SNP & Indel data with Hail MT, VCF, and PLINK.

Note: The ACAF Threshold smaller callsets were updated on 9/22/23 with an update to all three smaller callsets; more details can be found in this article. The new versions are referred to as version 7.1.

• Hail MT

WGS_ACAF_THRESHOLD_MULTI

_HAIL_PATH

Hail multiallelic MT for the ACAF threshold srWGS joint callset. Multiallelic sites are not split.

When using this file in Hail, read directly from the bucket location.  Do not attempt to copy it locally. Please see srWGS SNP & Indel Hail MT for more information.

• VCF

VCF for the ACAF threshold srWGS joint callset. This callset is converted from the ACAF Threshold Hail MT and sharded by chromosome into multiple files. 

Please see srWGS SNP & Indel VCFs for more information.

• Hail MT multiallelic split

WGS_ACAF_THRESHOLD_SPLIT

_HAIL_PATH

• Plink BED

gs://fc-aou-datasets-controlled/v7/wgs/short_read/snpindel/acaf_threshold_v7.1/plink_bed/

PLINK binary biallelic genotype table (.bed)  for the ACAF threshold srWGS joint callset. 

Includes .fam, .bim files for usage with the PLINK tool as well. These PLINK triplets are converted from the ACAF threshold  Hail MT.

• BGEN

gs://fc-aou-datasets-controlled/v7/wgs/short_read/snpindel/acaf_threshold_v7.1/bgen/

• UCSC BED

These subset files include srWGS SNP and Indel variants that are in Clinvar, not limited to  pathogenic or likely pathogenic variants. The ClinVar srWGS callset is provided in VCF, Hail MT, BGEN, and PLINK bed formats.

For more information on these subset files, please see Smaller callsets for analyzing srWGS SNP & Indel data with Hail MT, VCF, and PLINK.

Note: The ClinVar smaller callsets were updated on 9/22/23 with an update to all three smaller callsets; more details can be found in this article. The new versions are referred to as version 7.1.

• Hail MT

Hail MT for the ClinVar srWGS joint callset. Multiallelic sites are not split.

When using this file in Hail, read directly from the bucket location.  Do not attempt to copy it locally. Please see srWGS SNP & Indel Hail MT for more information.

• VCF

VCF for the ClinVar srWGS joint callset.

This callset is converted from the ACAF Threshold Hail MT and sharded by chromosome into multiple files. 

Please see srWGS SNP & Indel VCFs for more information.

• Hail MT multiallelic split

• PLINK BED

PLINK binary biallelic genotype table (.bed)  for the ClinVar srWGS joint callset. Includes .fam, .bim files for usage with the PLINK tool as well. 

These PLINK triplets are converted from the ClinVar Hail MT.

• BGEN

• UCSC BED

Path to manifest CSV file that contains a row per sample of: person_id,cram_uri,cram_index_uri

We provide CRAM files and CRAM index files with the research ID in the name of the file. One CRAM file for each WGS sample. See CRAM files for more information.

• srWGS SV VCF 

• srWGS SV sites-only VCF 

• aux

• srWGS SV samples with probable aneuploidies

• srWGS SV maximal set of unrelated samples

• srWGS PGx Haplotype v7

• srWGS PGx Haplotype v6

Single sample and joint called raw data, variant data, and auxiliary files. All single sample files are listed in the manifest, described in

Appendix 1. All other joint called and joint auxiliary files are listed below. 

• lrWGS single sample file manifest

The lrWGS manifest contains file locations for all single sample lrWGS raw data, variant data, and auxillary data. See

Appendix 1 for the description for each file.

Path to manifest CSV file that contains a row per sample of:

Research_id,hifiasm-primary-asm-fasta,hifiasm-hap1-asm-fasta,hifiasm-hap2-asm-fasta,hifiasm-primary-asm-gfa,hifiasm-hap1-asm-gfa,hifiasm-hap2-asm-gfa,hifiasm-quast-report-html,hifiasm-quast-report-summary,chm13v2.0-pav-vcf,chm13v2.0-pav-tbi,chm13v2.0-bam,chm13v2.0-bai,chm13v2.0-pbi,chm13v2.0-haplotagged-bam,chm13v2.0-haplotagged-bai,chm13v2.0-deepvariant-vcf,chm13v2.0-deepvariant-tbi,chm13v2.0-deepvariant-phased-vcf,chm13v2.0-deepvariant-phased-tbi,chm13v2.0-pbsv-vcf,chm13v2.0-pbsv-tbi,chm13v2.0-sniffles-vcf,chm13v2.0-sniffles-tbi,chm13v2.0-sniffles-snf,grch38-pav-vcf,grch38-pav-tbi,grch38-bam,grch38-bai,grch38-pbi,grch38-haplotagged-bam,grch38-haplotagged-bai,grch38-deepvariant-vcf,grch38-deepvariant-tbi,grch38-deepvariant-phased-vcf,grch38-deepvariant-phased-tbi,grch38-pbsv-vcf,grch38-pbsv-tbi,grch38-sniffles-vcf,grch38-sniffles-tbi,grch38-sniffles-snf

• Joint called Hail MT (grch38_noalt)

WGS_LONGREADS_HAIL_

GRCH38_PATH

Hail MT for the lrWGS joint callset for SNPs and Indels called to the grch38_noalt reference 

When using this file in Hail, read directly from the bucket location.  Do not attempt to copy it locally.

• Joint called Hail MT (T2Tv2.0)

Hail MT for the lrWGS joint callset for SNPs and Indels called to the T2Tv2.0 reference. 

When using this file in Hail, read directly from the bucket location.  Do not attempt to copy it locally.

Note: The joint-called Hail MT (T2Tv2.0) was updated to version 7.1 on 2/8/24.

• Joint called VCF (grch38_noalt)

WGS_LONGREADS_JOINT_SNP_

INDEL_VCF_GRCH38_PATH

Joint called lrWGS SNP and  Indel VCFagainst the grch38_noalt reference.

TBI index file accompanying the VCF is also provided.

• Joint called VCF (T2Tv2.0)

WGS_LONGREADS_JOINT_SNP_

INDEL_VCF_T2T_PATH

Joint called lrWGS SNP and  Indel VCF against the T2T-CHM13-v2.0 reference.

TBI index file accompanying the VCF is also provided.

• Aux (grch38_noalt)

• Aux (T2Tv2.0)

MICROARRAY_VCF_MANIFEST

_PATH

Path to manifest CSV file that contains a row per sample of: person_id,vcf_uri,vcf_index_uri

One VCF per participant sample.

Please see Array VCFs for more information.

Hail MT of the array samples in this release.  All of the samples have been merged into a single matrix table.  

Please see Array MatrixTable for more information. 

PLINK binary merged representation of the microarray samples in this release (.bed). Includes .fam, .bim files for usage with the plink tool as well. 

Please see Array PLINK 1.9 data for more information

gs://fc-aou-datasets-controlled/v7/microarray/idat/manifest.csv

MICROARRAY_IDAT_MANIFEST

_PATH

Path to manifest.csv file that contains a row per sample of: person_id,green_idat_uri,red_idat_uri

Two IDAT files per array sample with the research id in the name of the file. Please see IDAT files for more information.

gs://fc-aou-datasets-controlled/v7/known_issues/wgs_v7_not_in_cdr_known_issue_1.tsv

gs://fc-aou-datasets-controlled/v7/known_issues/array_v7_not_in_cdr_known_issue_1.tsv

gs://fc-aou-datasets-controlled/v7/wgs/short_read/structural_variants/v7_offcycle/aux/known_issues/AoU_srWGS_SV.v7_offcycle.not_in_cdr_known_issue_1.txt

gs://fc-aou-datasets-controlled/v7/known_issues/research_id_v7_array_known_issue_2.tsv

gs://fc-aou-datasets-controlled/v7/known_issues/research_id_v7_wgs_known_issue_2.tsv

gs://fc-aou-datasets-controlled/v7/known_issues/array_rids_v6_not_in_v7_known_issue_3.tsv

gs://fc-aou-datasets-controlled/v7/known_issues/research_id_v7_array_known_issue_14.tsv

gs://fc-aou-datasets-controlled/v7/known_issues/research_id_v7_array_known_issue_15.tsv

Each file contains a list of sample IDs associated with known issues.

For more information, please see All Of Us Release Genomic Quality Report (Known Issue #1,2,3,14,15)