tabix indexing a GTEx variant file- ':' delimited I have a gtex variant file- the head of which looks as follows:
phenotype_id                                    variant_id     
chr1:15947:16607:clu_36198:ENSG00000227232.5    chr1_13550_G_A_b38  ...
chr1:15947:16607:clu_36198:ENSG00000227232.5    chr1_14671_G_C_b38  ...
chr1:15947:16607:clu_36198:ENSG00000227232.5    chr1_14677_G_A_b38  ...
chr1:15947:16607:clu_36198:ENSG00000227232.5    chr1_16841_G_T_b38  ...

Effectively I would like to be able to lookup the variants inside a particular gene (the file is sorted) and put them in a temporary file:
E.g. If the variants in gene &quot;ENSG00000148481- MINDY3&quot; are on line number 87528225 to 87536766- effectively what I would like is the equivalent to zcat file.gz | sed -n '87528225,87536766p' &gt; MINDY3.txt. However zgrep ENSG00000148481 file.gz is just as fast as the above...
Hence I thought tabix would be the right tool for this-
I would like to tabix index it to make lookups faster. It is gzip compressed and I will firstly have to do:
zcat gtex.txt.gz | bgzip &gt; gtex.txt.bgz

However I am not quite sure how to proceed from there given that the data is not tab-delimited.
As a trial I tried the first 1000 lines:
zcat gtex.txt.gz | head -n 1000 | bgzip &gt; gtex_1000.txt.bgz

./tabix -p bed gtex_1000.gz #index as a bed file
[get_intv] the following line cannot be parsed and skipped: chr1:15947:16607:clu_36198:ENSG00000227232.5        chr1_13550_G_A_b38     ......

./tabix -p vcf gtex_1000.gz #index as a vcf file
Indexing as a bed file results in a warning while indexing as a vcf gives no warning yet either way when I try to retrieve a sequence:

./tabix test.gz chr1:15000:17000

It returns nothing.
I am starting to think that I will just have to write a script that splits on the ':' and writes the data to a new file.... and then index that file- which will take a huge amount of time
... Does anyone know of a trick to index the files with unconventional delimiting?
Tabix files need a name and a genomic coordinate at least. Tabix can be (ab)used by creating a fake genomic coordinate and then it just indexes names but not sure I would recommend this usage. What is your actual expected application of this?