latest-flat incorrectly displays non single-base substitution variants
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.
#1 Updated by Madeleine Ball about 8 years ago
This is related to the variants table having variant_aa_to/variant_aa_from for substitution variants and variant_aa_del / variant_aa_ins for indel variants. The aa_change and aa_change_short values in the flat_summary table json is incorrect.
Currently the genome GET-Evidence hit reports is broken for indel variants because flat_summary is broken; fixing this should fix these in the genome report.