Link to variant in ExAC even when no population data for the variant #846
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Yes, for a non-substitution variant (e.g. indel, copy number), the we would do a region search in ExAC for -30 to +30 each side of the variant. E.g http://exac.broadinstitute.org/region/12-112884023-112884083 : |
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thx @wrightmw - perfect. I couldn't read my scribbles :P |
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@selinad I'm having trouble reading mine! It's the luxury of having so much feedback from Steven. What a star! |
selinad
changed the title
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For a variant as the following: Which position should I be using for -30 and +30 in the region search? Thanks. |
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@jimmyzhen There is no definitive answer to this since there are any number of complex variant scenarios in the genome. My temptation in this instance would be to do -30 from the first number up to +30 for the second, e.g. 117120132 to 117120300 |
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@wrightmw, I was actually thinking about the same thing. Just wanted the confirmation. Thanks! |
Example variants for testingSubstitution variants (with both clinvar and cadd objects): Substitution variant (with only cadd object): Non-substitution variants (type "Duplication"): Non-substitution variants (type "Deletion"): Non-substitution variants (type "Insertion"): Non-substitution variants (type "Indel"): |
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You may review changes in the following instance: |
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@jimmyzhen @selinad Example variants for testingSubstitution variants (with both clinvar and cadd objects): Substitution variant (with only cadd object): Non-substitution variants (type "Duplication"): Non-substitution variants (type "Deletion"): Non-substitution variants (type "Insertion"): Non-substitution variants (type "Indel"): |
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Brilliant! Thanks, @wrightmw! |
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@selinad @jimmyzhen http://myvariant.info/v1/variant/chr1:g.957828A%3EC (CA501146) is not a good testing example because it is only GRCh38 and so does not currently return any ExAC population data The "indel" example (http://myvariant.info/v1/variant/chr7:g.117120152_117120270del119ins299 (VariationID: 53981)) has revealed a bug on the Basic Info tab where because of the long insertion in the HGVS names all the formatting of the page has been disrupted. Interestingly, none of the ClinVar data has been imported for this example (e.g. no ClinVar primary transcript and no RCV000047172)... I will make separate ticket for this:
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@wrightmw Aside from your comments above, did the changes in ticket work as expected for the external ExAC linkout? |
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@jimmyzhen Yes. Thanks. The ExAC link functionality worked well for the examples, except the CA ID one that could not render a link because it is GRCh38. That's why I created a new ticket for the wrapping issue because it's separate to your task on this ticket, which I think you have completed. |
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Further changes have been made for this ticket so that clicking on the "Search ExAC" link will take the user to ExAC's homepage when there is no data at all in the myvariant.info response. To review the changes, try CA501146 and CA501097 on the following new instance: I have also addressed the long HGVS term issues. Try 53981 and 90973 to review the fix. Thanks. |
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@jimmyzhen That's great Jimmy. Both examples work well now. Thanks. |
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Works well for me :-) |
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Great! |
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Included in last release (R7alpha2). Nice job and thanks for your hard work. |
Even when there is no variant data, curators would like to be able to link to the page when it is a subtitution - e.g.
1. For non-substitution variant (e.g. indel, copy number), do a region search ( @wrightmw did you get specification on this?)The text was updated successfully, but these errors were encountered: