Bug #492
closed
chrX data processing bugs
Description
In Chris Ball's processing of "Lilly Mendel" data from 23andme, I noticed there were no OMIM chrX results (but there were results in "other hypotheses", there is no SNPedia data though). I went and clickled on George's genome ( http://snp.med.harvard.edu/results/job/20/George_Church ) results and was shocked to find no chrX findings at all! (Maybe Jay Shendure was right, he's actually an alien.)
Looking over all the genomes, I get variable chrX findings, PGP1 and PGP4 have no chrX findings, and there are cases where OMIM or SNPedia chrX results are missing. While some of these could simply be because there are no findings to be had, it seems like the processing of chrX results needs to be checked.
No chrX results at all:
PGP1, PGP4
Other hypotheses only:
J Craig Venter (HuRef)
"Lilly Mendel": http://chris.printf.net/Lilly.html (SNPedia not
tested, raw data: http://chris.printf.net/genotype.dbsnp.gff )
SNPedia & Other hypotheses:
Seong-Jin Kim (SJK)
OMIM & Other hypotheses:
PGP11
Stephen Quake (P0)
OMIM & SNPedia & Other hypotheses:
Desmond Tutu (ABT), Ai, etc.
James Watson (JW)
NA18507
NA19240
NA07022
Updated by Madeleine Ball almost 16 years ago
Here's a version of the Lilly Mendel query with working snpedia results:
http://chris.printf.net/Lilly-with-snpedia.html
There are three chrX matches in snpedia (and three in Other Hypotheses), which suggests that at least for this search, it's only the OMIM backend that isn't finding chrX matches.
Updated by Ward Vandewege about 15 years ago
- Project changed from 19 to GET-Evidence
- Category deleted (
GET-Evidence)
Updated by Madeleine Ball about 15 years ago
- Status changed from New to Closed
This is largely obsoleted by the movement of Trait-o-matic code into Get-Evidence. In particular, 2cf1c939 removed the omim filter. Because GET-Evidence has all OMIM variants already imported, we now use it to detect if a variant is in OMIM. SNPedia is no longer used (but could be added back in later).
Checking output for PGP1 right now, I see that there is a chrX finding from OMIM (HTR2C-C23S).