Use variable to change flag to cut command in bash

I have a file test.geno.file.txt which contains chromosome and alleles and some numbers in it (this one is SPACE separated, but I have another which is TAB separated):

marker allele1 allele2 id1 id1 id2 id2
chr11_96001606 C T 1.25893e-12 1 3.16228e-26 0.000999001
chr1_46021459 G T 0.969347 0.0306534 1.22034e-21 0.996035

I'm using a script that checks if it is tab or space delimited and stores the result inside the FILESEPvariable:

file=~/Desktop/test.geno.file.txt
  
  if cat $file | awk '{exit !/\t/}'; then
  echo "Tab delimited" # tab file
  FILESEP=""
  else
    FILESEP="-d \ "
  echo "Space delimited with $FILESEP" # space file
  fi
  onlyfile=$(basename $file)

Basically, I want to modify the original file to get the chromosome names and positions separated. I'm using the cut command, but I would like to make it easier to change the delimiter flag (using the if statement and variable above)

Like this:

  POSFILE=${onlyfile%.txt}.pos.gz # Next command will generate it 
  cat $file | cut -d' '  -f 1 | perl -p -e 's/_([^_]+$)/\t$1/' | grep -v marker | gzip > ~/Desktop/$POSFILE # Keep position only chr \t pos 

This is the output:

gunzip -c ~/Desktop/$POSFILE

chr11   96001606
chr1    46021459

But changing the -d' ' with $FILESEP:

  cat $file | cut $FILESEP  -f 1 | perl -p -e 's/_([^_]+$)/\t$1/' | grep -v marker | gzip > ~/Desktop/$POSFILE # Keep position only chr \t pos 

But this last command doesn't work...

Assuming none of the fields contain spaces, I'd replace cut with awk where the default delimiter is white space (space, contiguous spaces, tab, contiguous tabs). This would do away with the whole if/then/else construct do determine what to put in FILESEP.
In other words ...

Replace this:

if cat $file | awk '{exit !/\t/}'; then
    echo "Tab delimited" # tab file
    FILESEP=""
else
    FILESEP="-d \ "
    echo "Space delimited with $FILESEP" # space file
fi
....
cat $file | cut $FILESEP -f 1 | perl ...

With this:

awk '{print $1}' "${file}" | perl ...

# or if using zcat (per one of OP's comments)

zcat "${file}" | awk '{print $1}' | perl ...

NOTE: I don't work with perl but I'd be surprised if you couldn't emulate this awk script inside perl (ie, eliminate the awk call with some additional code in the perl script) ... ??

Quoting is crucial when expanding parameters. Not quoting a parameter when expanding is almost always an error and shellcheck will rightfully complain about it.

The solution in this case is to always specify the delimiter:

if awk '{exit !/\t/}' "$file"; then
  FILESEP='	' # a literal tab character. In terminal, enter by pressing Ctrl-v Tab, or Ctrl-v Ctrl-i
else
  FILESEP=' '
fi
cut -d "$FILESEP" -f1 yourfile