Project

General

Profile

Actions

Bug #468

open

latest-flat incorrectly displays non single-base substitution variants

Added by Madeleine Ball almost 12 years ago. Updated almost 12 years ago.

Status:
New
Priority:
High
Assigned To:
-
Target version:
-
Start date:
02/15/2011
Due date:
% Done:

0%

Estimated time:
Billable:
Estimatedhours:
Hours:
Totalhours:
Resolution:
Story points:
-

Description

I haven't checked, but this problem likely extends to deletion & other new length changing or multiple-aa variants.

This bug blocks creating a flatfile version of gff_getevidence_map.py

For example, FIG4-K278Shift is showing up like this (2nd and 3rd columns are incorrect):
FIG4 278 278 pathogenic Moderate clinical importance, Uncertain pathogenic recessive 0 0 0 0 0 3 Y -- - Y 0 Y 3 - 2 - Y - - - - Y 4 Y 2N 1 0 This variant is predicted to cause a frameshift and may cause Charcot-Marie-Tooth Disease Type 4J in an autosomal recessive manner. Other variants in this gene which cause frameshift and premature termination have been implicated in causing this disease when compound heterozygous with another FIG4 variant.

While MYL2-A13T shows up like this:
MYL2 Ala13Thr A13T pathogenic Low clinical importance, Uncertain pathogenic dominant 1 1 1 6 6 3 Y 4Y 0 Y ! Y 4 Y 3 Y Y Y - - Y Y 1 - Familial Hypertrophic Cardiomyopathy 4596 1 455 3.054 4 N 0 0 This rare variant is implicated in causing late-onset familial hypertrophic cardiomyopathy. The variant has been found in five affected Caucasian individuals (in four families), but affected non-carriers and unaffected carriers have also been observed. No statistically significant enrichment of this variant in cases vs. controls has been shown.

Actions

Also available in: Atom PDF