Does BWA-MEM 2 account for overlapping reads within the paired end data?

Question

[ayeraselvan]

Does the variant calling is affected when we have some overlapping reads within the paired end reads? I am planning to use variant calling using GATK but I am mapping with Bwa-mem2

Answer 1

[LChart]

Yes, GATK variant calling understands that a base mismatch in overlapping reads from the same read pair is actually derived just from observation of the underlying molecule.

[ayeraselvan]

Thank you! Have a nice day :)