Feature #578

Improve reporting of variant/allele frequencies

Added by Tom Clegg about 8 years ago. Updated about 8 years ago.

Status:
Feedback
Priority:
Normal
Assigned To:
-
Target version:
-
Start date:
05/19/2011
Due date:
% Done:

100%

Estimated time:
Billable:
Estimatedhours:
Hours:
Totalhours:
Resolution:
fixed
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?

History

#1 Updated by Tom Clegg about 8 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

Also available in: Atom PDF