AndersenLab / annotation-nf

Annotate VCF with snpeff and bcsq
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% Protein Calculation for CB is returning >100% Protein Length for CB annos #7

Open mckeowr1 opened 1 year ago

mckeowr1 commented 1 year ago

An example from the most recent annotation run:

7010 C T missense QX1410.4943 QX1410.4943.1 protein_coding - 680M>680I 7010C>T QG3923 1 10 286.92*
mckeowr1 commented 1 year ago

This is because the % protein calculations require a key file defined as a static parameter. The key file (AA_length.tsv) is older than the GFF and the unique IDs for transcripts have been re-generated. We are referencing old protein lengths. The code to generate the key file is not included in the pipeline ATM