I am currently trying to set up the LOEUF plugin for the VEP tool and have run into a few problems.

The ensembl website (see "more" under LOEUF) specifies that, before the processing (for GRCh38) the file (downloaded here (constraint metrics)) needs the start and end position.

I have been doing that by essentially running the R code ensembl provides to lookup gene symbols with a map function (bc I do not know perl but using the API in R vs perl shouldn't differ, right? Also I used the symbols, not the transcripts, as the transcripts in the file were often RefSeq transcripts and I couldn't get that to work). All of that worked up until I wanted to process my file as specified on the website:

cat gnomad.v4.1.constraint_metrics_with_coordinates.tsv | (head -n 1 && tail -n +2  | sort -t$'\t' -k 53,53 -k 56,56n ) > loeuf_grch38_temp.tsv
sed '1s/.*/#&/' loeuf_grch38_temp.tsv > loeuf_dataset_grch38.tsv
bgzip loeuf_dataset_grch38.tsv
tabix -f -s 53 -b 56 -e 57 loeuf_dataset_grch38.tsv.gz

Then at the very end the tabix did not work and I realized the file I downloaded (Constraint metrics TSV via Google) had 113 columns to begin with, including start_position and end_position as columns no.9,10 and 11 or smth like that (which have alot of N/A so they don't have a chr,start and end for every transcript but so be it).

Now because I am an absolute newbie at bioinformatics, a few questions arose:

1.Can I just change the columns referred to in the processing sort and tabix command to the numbers of my columns or would that, in the future disrupt my LOEUF plugin?

2.Is the information for the LOEUF plugin on ensembl's website just outdated and that's why the amount of columns didn't match or did I download the wrong file?

3.can and should I use biomaRt to assign the chr, start and end in the first place? As far as I understand I could get the information for the transcript, not just the symbols easily that way but I am wondering If that is even necessary for LOEUF at the end or if what I did would work just fine in this case.

4.If the file has just been updated and therefor not includes the coordinates on the broadinstitute website at download already, can I just adjust the sort and tabix to those columns? That would be the easiest by far :D!

To whoever read through this and might answer: you're a true soldier and I thank you for your service!