detect and combine indels into one line like Mutect2 format

Question

[whb]

Hi,

I would like to get a list of common SNVs and indels from two variant callers (Mutect2 and lofreq). but lofreq output indels as two SNVs whereas Mutect2 output indels as one line (shown below) and bcftools -isec does not recognise they are the same.

How can I combine the indels SNVs in the lofreq vcfs into one line like the format in Mutect2?

lofreq vcf:

chr5    117401004   .   G   A
chr5    117401005   .   G   T

Mutect vcf

chr5    117401004   .   GG  AT

Thank you!