Hi

I guess I have a rather simple problem but I couldn't find a solution in previous answers. From the "COVID19hg" GWAS consortium, I am trying to extract all SNPs that intersect with the coordination of a list of genes I'm interested in. I understand it's normally done with tools like bedtools intersect but the issue is that the GWAS results are not reported in a standard vcf format, and they only allow to download the file in a text format similar to vcf but with no headers and many additional columns. See the head of one example file:

(base)$ head COVID19_HGI_B1_ALL_leave_23andme_20210607.b37.txt 
#CHR    POS REF ALT SNP all_meta_N  all_inv_var_meta_beta   all_inv_var_meta_sebeta all_inv_var_meta_p  all_inv_var_meta_cases  all_inv_var_meta_controls   all_inv_var_meta_effective  all_inv_var_het_p   all_meta_AF rsid    anew_chr    anew_pos    REF ALT
1   693731  A   G   1:693731:A:G    12  -2.5351e-02 3.3686e-02  4.5172e-01  7077    51575   5827    4.1912e-01  1.249e-01   rs12238997  1   758351  A   G
1   714596  T   C   1:714596:T:C    7   -3.3903e-02 7.0748e-02  6.3179e-01  5743    41335   4676    8.8309e-01  3.347e-02   rs149887893 1   779216  T   C
1   715265  C   T   1:715265:C:T    8   -4.1206e-02 6.4139e-02  5.2059e-01  6213    41615   4851    9.0075e-01  3.687e-02   rs12184267  1   779885  C   T
1   715367  A   G   1:715367:A:G    8   -3.1029e-02 6.4021e-02  6.2791e-01  6213    41615   4851    8.7083e-01  3.7e-02 rs12184277  1   779987  A   G
1   717485  C   A   1:717485:C:A    8   -3.705e-02  6.4596e-02  5.6626e-01  6213    41615   4851    8.8184e-01  3.664e-02   rs12184279  1   782105  C   A
1   717587  G   A   1:717587:G:A    5   -3.2116e-02 1.0398e-01  7.5743e-01  5588    39337   4555    9.8982e-02  1.464e-02   rs144155419 1   782207  G   A
1   720381  G   T   1:720381:G:T    8   -3.5517e-02 6.3729e-02  5.7732e-01  6213    41615   4851    8.9083e-01  3.732e-02   rs116801199 1   785001  G   T
1   721290  G   C   1:721290:G:C    8   -3.5073e-02 6.3631e-02  5.8151e-01  6213    41615   4851    8.6413e-01  3.747e-02   rs12565286  1   785910  G   C
1   723891  G   C   1:723891:G:C    7   1.6154e-02  5.4698e-02  7.6774e-01  5666    42317   4650    7.5031e-01  9.479e-01   rs2977670   1   788511  G   C

Now I am trying to intersect this SNPs report file with a GTF annotation file that I have already filtered for my genes of interest. However bedtools does not recognise the SNP report file as a valid entry. I tried to make the file look like a vcf format to be compatible but the trick did not work:

(base)$ bedtools intersect -a COVID19_HGI_B1_ALL_leave_23andme_20210607.b37.vcf -b shortlistGTF.gtf -wa -wb 
Error: unable to open file or unable to determine types for file COVID19_HGI_B1_ALL_leave_23andme_20210607.b37.vcf

- Please ensure that your file is TAB delimited (e.g., cat -t FILE).
- Also ensure that your file has integer chromosome coordinates in the 
  expected columns (e.g., cols 2 and 3 for BED).

Is there any way to input custom txt files (other than BED/VCF/GTF formats) in bedtools and provide argument which columns/fields need to be used for the intersection? I'm quite open to options other than bedtools as well, PICARD, etc. Thank you very much!