Links to external websites from seqr are not working as expected for various external website. These issues are universal, impacting every variant in every project (as far as I can tell). Here is a list:
Shows the frequency of the variant in gnomAD v2 and should link out to gnomAD v2: The numbers here correctly show the number of alleles for gnomAD v2, though the frequency is incorrect (showing European frequency maybe?) and the link out is for gnomAD v4. In the example, the link in seqr is https://gnomad.broadinstitute.org/variant/1-46642089-AG-A, which returns 'Variant not found' because 1-46642089-AG-A are the hg19 co-ordinates and gnomAD v4 requires hg38 co-ordinates in the URL parameters. The link seqr should be showing for this example is https://gnomad.broadinstitute.org/variant/1-46642089-AG-A?dataset=gnomad_r2_1 and the frequency seqr should be showing is 0.000016.
Should link out to the variant in Iranome: The URL parameters for this website are expecting the co-ordinates in hg19 but seqr is providing hg38 co-ordinates. See issue #177 for a detailed example.
Should link out to the variant in Geno2MP: The URL parameters for this website are expecting the co-ordinates in hg19 but seqr is providing hg38 co-ordinates. See issue #177 for a detailed example.
1 and 2 are the most important to fix as our collaborators click on these all the time and it's currently very confusing.
Links to external websites from seqr are not working as expected for various external website. These issues are universal, impacting every variant in every project (as far as I can tell). Here is a list:
Shows TopMed data and links out to Bravo: The numbers here correctly show frequency data for TopMed freeze 8 but the link is to TopMed freeze 5. In the example shown, the link in seqr is https://bravo.sph.umich.edu/freeze5/hg38/variant/1-46176417-AG-A which links to an error page because the variant not present in freeze 5. The correct link seqr should be showing is https://bravo.sph.umich.edu/freeze8/hg38/variant/snv/1-46176417-AG-A
Shows the frequency of the variant in gnomAD v2 and should link out to gnomAD v2: The numbers here correctly show the number of alleles for gnomAD v2, though the frequency is incorrect (showing European frequency maybe?) and the link out is for gnomAD v4. In the example, the link in seqr is https://gnomad.broadinstitute.org/variant/1-46642089-AG-A, which returns 'Variant not found' because 1-46642089-AG-A are the hg19 co-ordinates and gnomAD v4 requires hg38 co-ordinates in the URL parameters. The link seqr should be showing for this example is https://gnomad.broadinstitute.org/variant/1-46642089-AG-A?dataset=gnomad_r2_1 and the frequency seqr should be showing is 0.000016.
Should link out to the gnomAD v2 gene page for this variant: Links out to the gnomAD v4 page instead. In the example, the link in seqr is https://gnomad.broadinstitute.org/gene/ENSG00000250719 but it should be https://gnomad.broadinstitute.org/gene/ENSG00000250719?dataset=gnomad_r2_1. As an aside, there is a Broad seqr GitHub ticket where they are looking into adding gnomAD v4 to seqr. If the broad update seqr to include v4, these links might be fixed up then? Unless this issue is separate to the Broad's code.
Should link out to the protein/genomic info tab for the gene in Decihper: Clicking on this link currently takes you to the decipher home page https://www.deciphergenomics.org/. In the example, this link should be https://www.deciphergenomics.org/gene/P3R3URF/overview/protein-genomic-info
Should link out to the variant in Iranome: The URL parameters for this website are expecting the co-ordinates in hg19 but seqr is providing hg38 co-ordinates. See issue #177 for a detailed example.
Should link out to the variant in Geno2MP: The URL parameters for this website are expecting the co-ordinates in hg19 but seqr is providing hg38 co-ordinates. See issue #177 for a detailed example.
1 and 2 are the most important to fix as our collaborators click on these all the time and it's currently very confusing.
Thanks!