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Feature #578
open
Improve reporting of variant/allele frequencies
Status:
Feedback
Priority:
Normal
Assigned To:
-
Target version:
-
Story points:
-
Description
Pieces:
- Current data on evidence.personalgenomes.org seems to have been imported from "all.txt" (should have used "parsed_for_getev.txt") in mball data
- Better version of parsed_for_getev.txt is available too
- Should not use sum(num)/sum(denom) because many of the same genomes are included in multiple populations (hapmap, 1000g, cgi)
- Just use local genomes, and generate a report of variants whose frequencies differ wildly from 1000genomes/hapmap?
Updated by Tom Clegg almost 13 years ago
- Status changed from In Progress to Feedback
- % Done changed from 0 to 100
- Resolution set to fixed
Done:
- Fixed update_variant_frequency.php to use population with highest denominator, instead of summing populations (985000, ec7159)
- Updated import_variant_frequency.php to use "for getev" format (ea8475c) -- also, look up "unknown" variant_ids using variant_name
- Imported parsed_for_getev_new.txt from mball on production site. E.g., COL4A1-Q1334H, ATAD3C-A91V
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