split 1 column input into 5 column bed file
The following Python script seems to do the job.

#!/usr/bin/env python3

from __future__ import print_function
import re
import sys

for line in sys.stdin:
    if '_' in line:
        match = re.search(r'(\S+):(\d+)_(\d+)del([ACGT]+)ins([ACGT]+)', line)
        print(match.group(1), match.group(2), match.group(3), match.group(5), match.group(4), sep='\t')
    elif 'dup' in line or 'del' in line:
        match = re.search(r'(\S+):(\d+)(del|dup)([ACGT]+)', line)
        if match.group(3) == 'del':
            print(match.group(1), match.group(2), match.group(2), match.group(4), '-', sep='\t')
        else:
            print(match.group(1), match.group(2), match.group(2), '-', match.group(4), sep='\t')
    else:
        match = re.search(r'(\S+):(\d+)([ACGT]+)&gt;([ACGT]+)', line)
        coord = int(match.group(2))
        print(match.group(1), coord - 1, coord, match.group(3), match.group(4), sep='\t')


Invoked like so on the command line.

[standage@lappy ~] $ ./transform &lt; f1
chr7 140453144 140453145 A T
chr7 140453135 140453136 A T
chr7    140453135   140453136   TT  CA
chr20   31022287    31022287    -   A
chr19   13054614    13054614    G   -