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Update HGDP/1KG tutorial download links #1533

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merged 3 commits into from
May 6, 2024
Merged

Update HGDP/1KG tutorial download links #1533

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9e882b0
fix(browser): update v4.1 SV and CNV download hashes and sizes
rileyhgrant May 2, 2024
0e5664c
refactor(browser): generalize download links associated files
rileyhgrant May 2, 2024
a9ee50f
feat(browser): update hgdp tutorial download links
rileyhgrant May 2, 2024
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2 changes: 1 addition & 1 deletion browser/src/DownloadsPage/ExacDownloads.tsx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@ const ExacDownloads = () => (
path="/legacy/exac_browser/ExAC.r1.sites.vep.vcf.gz"
size="4.56 GiB"
md5="f2b57a6f0660a00e7550f62da2654948"
includeTBI
associatedFileType="TBI"
/>
</ListItem>
</FileList>
Expand Down
22 changes: 11 additions & 11 deletions browser/src/DownloadsPage/GnomadV2Downloads.tsx
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -212,7 +212,7 @@ const GnomadV2Downloads = () => {
path="/release/2.1.1/vcf/exomes/gnomad.exomes.r2.1.1.sites.vcf.bgz"
size="58.81 GiB"
md5="f034173bf6e57fbb5e8ce680e95134f2"
includeTBI
associatedFileType="TBI"
/>
</ListItem>
{exomeChromosomeVcfs.map(({ chrom, size, md5 }) => (
Expand All @@ -223,7 +223,7 @@ const GnomadV2Downloads = () => {
path={`/release/2.1.1/vcf/exomes/gnomad.exomes.r2.1.1.sites.${chrom}.vcf.bgz`}
size={size}
md5={md5}
includeTBI
associatedFileType="TBI"
/>
</ListItem>
))}
Expand All @@ -247,7 +247,7 @@ const GnomadV2Downloads = () => {
path="/release/2.1.1/vcf/genomes/gnomad.genomes.r2.1.1.sites.vcf.bgz"
size="460.93 GiB"
md5="e6eadf5ac7b2821b40f350da6e1279a2"
includeTBI
associatedFileType="TBI"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
Expand All @@ -257,7 +257,7 @@ const GnomadV2Downloads = () => {
path="/release/2.1.1/vcf/genomes/gnomad.genomes.r2.1.1.exome_calling_intervals.sites.vcf.bgz"
size="9.7 GiB"
md5="e5bd69a0f89468149bc3afca78cd5acc"
includeTBI
associatedFileType="TBI"
/>
</ListItem>
{genomeChromosomeVcfs.map(({ chrom, size, md5 }) => (
Expand All @@ -268,7 +268,7 @@ const GnomadV2Downloads = () => {
path={`/release/2.1.1/vcf/genomes/gnomad.genomes.r2.1.1.sites.${chrom}.vcf.bgz`}
size={size}
md5={md5}
includeTBI
associatedFileType="TBI"
/>
</ListItem>
))}
Expand Down Expand Up @@ -331,47 +331,47 @@ const GnomadV2Downloads = () => {
<DownloadLinks
label="SV 2.1 sites VCF"
path="/papers/2019-sv/gnomad_v2.1_sv.sites.vcf.gz"
includeTBI
associatedFileType="TBI"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="SV 2.1 sites BED"
path="/papers/2019-sv/gnomad_v2.1_sv.sites.bed.gz"
includeTBI
associatedFileType="TBI"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="SV 2.1 (controls) sites VCF"
path="/papers/2019-sv/gnomad_v2.1_sv.controls_only.sites.vcf.gz"
includeTBI
associatedFileType="TBI"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="SV 2.1 (controls) sites BED"
path="/papers/2019-sv/gnomad_v2.1_sv.controls_only.sites.bed.gz"
includeTBI
associatedFileType="TBI"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="SV 2.1 (non-neuro) sites VCF"
path="/papers/2019-sv/gnomad_v2.1_sv.nonneuro.sites.vcf.gz"
includeTBI
associatedFileType="TBI"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="SV 2.1 (non-neuro) sites BED"
path="/papers/2019-sv/gnomad_v2.1_sv.nonneuro.sites.bed.gz"
includeTBI
associatedFileType="TBI"
/>
</ListItem>
</FileList>
Expand Down
8 changes: 4 additions & 4 deletions browser/src/DownloadsPage/GnomadV2LiftoverDownloads.tsx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -109,7 +109,7 @@ const Gnomadv2LiftoverDownloads = () => {
path="/release/2.1.1/liftover_grch38/vcf/exomes/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.bgz"
size="85.31 GiB"
md5="cff8d0cfed50adc9211d1feaed2d4ca7"
includeTBI
associatedFileType="TBI"
/>
</ListItem>
{liftoverExomeChromosomeVcfs.map(({ chrom, size, md5 }) => (
Expand All @@ -120,7 +120,7 @@ const Gnomadv2LiftoverDownloads = () => {
path={`/release/2.1.1/liftover_grch38/vcf/exomes/gnomad.exomes.r2.1.1.sites.${chrom}.liftover_grch38.vcf.bgz`}
size={size}
md5={md5}
includeTBI
associatedFileType="TBI"
/>
</ListItem>
))}
Expand All @@ -144,7 +144,7 @@ const Gnomadv2LiftoverDownloads = () => {
path="/release/2.1.1/liftover_grch38/vcf/genomes/gnomad.genomes.r2.1.1.sites.liftover_grch38.vcf.bgz"
size="743.06 GiB"
md5="83de3d5b52669f714e810d4fcf047c18"
includeTBI
associatedFileType="TBI"
/>
</ListItem>
{liftoverGenomeChromosomeVcfs.map(({ chrom, size, md5 }) => (
Expand All @@ -155,7 +155,7 @@ const Gnomadv2LiftoverDownloads = () => {
path={`/release/2.1.1/liftover_grch38/vcf/genomes/gnomad.genomes.r2.1.1.sites.${chrom}.liftover_grch38.vcf.bgz`}
size={size}
md5={md5}
includeTBI
associatedFileType="TBI"
/>
</ListItem>
))}
Expand Down
88 changes: 63 additions & 25 deletions browser/src/DownloadsPage/GnomadV3Downloads.tsx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -116,7 +116,7 @@ const GnomadV3Downloads = () => (
path={`/release/3.1.2/vcf/genomes/gnomad.genomes.v3.1.2.sites.chr${chrom}.vcf.bgz`}
size={size}
md5={md5}
includeTBI
associatedFileType="TBI"
/>
</ListItem>
))}
Expand Down Expand Up @@ -195,7 +195,7 @@ const GnomadV3Downloads = () => (
<ListItem>
<DownloadLinks
label="Sample metadata TSV"
path="/release/3.1.2/vcf/genomes/gnomad.genomes.v3.1.2.hgdp_1kg_subset_sample_meta.tsv.bgz"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/metadata_and_qc/gnomad_meta_updated.tsv"
/>
</ListItem>
{hgdpAnd1kgChromosomeVcfs.map(({ chrom, size, md5 }) => (
Expand All @@ -206,7 +206,7 @@ const GnomadV3Downloads = () => (
path={`/release/3.1.2/vcf/genomes/gnomad.genomes.v3.1.2.hgdp_tgp.chr${chrom}.vcf.bgz`}
size={size}
md5={md5}
includeTBI
associatedFileType="TBI"
/>
</ListItem>
))}
Expand Down Expand Up @@ -238,7 +238,7 @@ const GnomadV3Downloads = () => (
path="/release/3.1/vcf/genomes/gnomad.genomes.v3.1.sites.chrM.vcf.bgz"
size="4.77 MiB"
md5="d0ef2bd882ae44236897d743cb5528cf"
includeTBI
associatedFileType="TBI"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
Expand Down Expand Up @@ -435,86 +435,100 @@ const GnomadV3Downloads = () => (
<ListItem>
<DownloadLinks
label="Sample metadata TSV"
path="/release/3.1/secondary_analyses/hgdp_1kg/metadata_and_qc/gnomad_meta_v1.tsv"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/metadata_and_qc/gnomad_meta_v1.tsv"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Subset of the HGDP+1KG callset MatrixTable"
path="/release/3.1/secondary_analyses/hgdp_1kg/pca_preprocessing/ld_pruned.mt"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/pca_preprocessing/ld_pruned.mt"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Related sample IDs Hail Table"
path="/release/3.1/secondary_analyses/hgdp_1kg/pca_preprocessing/related_sample_ids.ht"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/pca_preprocessing/related_sample_ids.ht"
/>
</ListItem>

{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Principal component analysis (PCA) PC score tables GCS Bucket"
path="/release/3.1/secondary_analyses/hgdp_1kg/pca/pc_scores_with_outliers/"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/pca/pc_scores_with_outliers/"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="PCA outliers table"
path="/release/3.1/secondary_analyses/hgdp_1kg/pca/pca_outliers.txt"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/pca/pca_outliers.txt"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="PCA PC score tables without outliers GCS Buckets"
path="/release/3.1/secondary_analyses/hgdp_1kg/pca/pc_scores_without_outliers/"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/pca/pc_scores_without_outliers/"
/>
</ListItem>

{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Variants and unrelated samples MatrixTable"
path="/release/3.1/secondary_analyses/hgdp_1kg/pca_results/unrelateds_without_outliers.mt"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/pca_results/unrelateds_without_outliers.mt"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Variants and related samples MatrixTable"
path="/release/3.1/secondary_analyses/hgdp_1kg/pca_results/relateds_without_outliers.mt"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/pca_results/relateds_without_outliers.mt"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="Population-level statistical summary TSV"
path="/release/3.1/secondary_analyses/hgdp_1kg/metadata_and_qc/post_qc_summary.tsv"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/metadata_and_qc/post_qc_summary.tsv"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="Doubleton counts CSV"
path="/release/3.1/secondary_analyses/hgdp_1kg/f2_fst/doubleton_count.csv"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/f2_fst/doubleton_count.csv"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Variants and unrelated sample PLINK files"
path="/release/3.1/secondary_analyses/hgdp_1kg/f2_fst/hgdp_tgp*"
label="Variants and unrelated sample PLINK files - .bed"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/f2_fst/hgdp_tgp.bed"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Variants and unrelated sample PLINK files - .bim"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/f2_fst/hgdp_tgp.bim"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Variants and unrelated sample PLINK files - .fam"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/f2_fst/hgdp_tgp.fam"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="Population-level mean fixation index table"
path="/release/3.1/secondary_analyses/hgdp_1kg/f2_fst/mean_fst.txt"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/f2_fst/mean_fst.txt"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
Expand Down Expand Up @@ -542,7 +556,7 @@ const GnomadV3Downloads = () => (
<ListItem>
<GetUrlButtons
label="HGDP+1KG and GVV intersection Matrix Table"
path="/release/3.1/secondary_analyses/hgdp_1kg/data_intersection/hgdp_tgp_ggv_intersect.mt"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/data_intersection/hgdp_tgp_ggv_intersect.mt"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
Expand All @@ -565,21 +579,21 @@ const GnomadV3Downloads = () => (
<ListItem>
<GetUrlButtons
label="Pre-QC column fields Hail Table"
path="/release/3.1/secondary_analyses/hgdp_1kg/plot_datasets/pre_qc_plotting.ht"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/plot_datasets/pre_qc_plotting.ht"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Pre-QC expected heterozygosity Hail Table"
path="/release/3.1/secondary_analyses/hgdp_1kg/plot_datasets/expected_hets_pre_qc.ht"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/plot_datasets/expected_hets_pre_qc.ht"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Pre-QC actual heterozygosity Hail Table"
path="/release/3.1/secondary_analyses/hgdp_1kg/plot_datasets/actual_hets_pre_qc.ht"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/plot_datasets/actual_hets_pre_qc.ht"
/>
</ListItem>

Expand All @@ -588,28 +602,52 @@ const GnomadV3Downloads = () => (
<ListItem>
<GetUrlButtons
label="Post-QC column fields Hail Table"
path="/release/3.1/secondary_analyses/hgdp_1kg/plot_datasets/post_qc_plotting.ht"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/plot_datasets/post_qc_plotting.ht"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Post-QC expected heterozygosity Hail Table"
path="/release/3.1/secondary_analyses/hgdp_1kg/plot_datasets/expected_hets_post_qc.ht"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/plot_datasets/expected_hets_post_qc.ht"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Post-QC actual heterozygosity Hail Table"
path="/release/3.1/secondary_analyses/hgdp_1kg/plot_datasets/actual_hets_post_qc.ht"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/plot_datasets/actual_hets_post_qc.ht"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="Post-QC site frequency spectrum table"
path="/release/3.1/secondary_analyses/hgdp_1kg/plot_datasets/sfs_post_qc.txt"
path="/release/3.1/secondary_analyses/hgdp_1kg_v2/plot_datasets/sfs_post_qc.txt"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="Phased haplotype ChrX PAR1"
path="/resources/hgdp_1kg/phased_haplotypes_v2/hgdp1kgp_chrX_par1.shapeit5_common.bcf"
associatedFileType="CSI"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="Phased haplotype ChrX PAR2"
path="/resources/hgdp_1kg/phased_haplotypes_v2/hgdp1kgp_chrX_par2.shapeit5_common.bcf"
associatedFileType="CSI"
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="Phased haplotype ChrX Non-PAR"
path="/resources/hgdp_1kg/phased_haplotypes_v2/hgdp1kgp_chrX_non_par.full.shapeit5_rare.bcf"
associatedFileType="CSI"
/>
</ListItem>
</FileList>
Expand Down
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