Mane Plus Clinical tags missing from gff.json.gz files

[holtgrewe]

For cdot v0.2.22 and v0.2.23, it holds true that cdot-$VERSION.GCF_000001405.40_GRCh38.p14_genomic.110.gff.json.gz contain MANE Select but not MANE Plus Clinical tags.

The MANE Plus Clinical tags are in the cdot-0.2.22.refseq.grch38.json.gz and cdot-0.2.22.ensembl.Homo_sapiens.GRCh38.110.gff3.json.gz files, however.

[holtgrewe]

I am not 100% certain that I understand how the transcripts are built. However, it appears that multiple GFF files are merged for historical transcripts. In the case of a transcripts with the same accession in version being in two different GFF files from NCBI and one has a tag while the other does not - which one wins? The first one or the last one?

[davmlaw]

cdot-$VERSION.GCF_000001405.40_GRCh38.p14_genomic.110.gff.json.gz contain MANE Select but not MANE Plus Clinical tags.

There are no "MANE Plus" tags in the original GFF file for the .json.gz produced above

$ zgrep -l "MANE Plus" *.gff.gz

GCF_000001405.40_GRCh38.p14_genomic.RS_2023_03.gff.gz
GCF_000001405.40_GRCh38.p14_genomic.RS_2023_10.gff.gz
GCF_000001405.40-RS_2023_03_combined_annotation_alignments.gff.gz
GCF_000001405.40-RS_2023_03_genomic.gff.gz

So the MANE Plus clinical tags appear in json.gz files where the GFF had the tag, or in merged historical ones

which one wins? The first one or the last one?

The last one. The idea is that the latest will have corrected the earlier one