What is indel calling and what is its purpose? I'm having a difficulty in grasping the general purpose and concept of indel calling.

What exactly is this process?
There are two types of INDELs: short indels and long indels. Some put the threshold at 50bp; others choose 1000bp. Short and long indels are called differently.

&lt;50bp short indels are called from read alignment directly. Modern indel callers essentially build a multi-alignment of reads and call an indel with enough read supports. Short indels may break open reading frames.

For Illumina reads, long indels are usually called with split alignment or read pair alignment because mainstream aligners are unable to directly align through a long indel. Long indels are a type of structural variation. They may affect gene structures in a more dramatic way (e.g. delete a whole exon; screw up transcription by transposon insertion; create pseudogenes).

Ultimately, both short and long indels are types of genetic variants. Calling them helps to understand how genetics shapes phenotypes.