What type of duplicates are to be removed while analyzing whole exome data?

Question

[vinayjrao]

Hi,

I am analyzing whole exome data to analyze InDels and SNPs between healthy control and diseased patients. Since I'm new to analyzing exome data, I would like to know whether I should remove all duplicates or only sequencing duplicates, because removing all duplicates can also result in neglecting the genomic duplication events.

Thanks in advance.

[ATpoint]

If you have no experience I recommend using a standard and published workflow for exome data analysis rather than putting things together yourself. As inspiration e.g. https://github.com/gatk-workflows/gatk4-exome-analysis-pipeline