How to detect insertion and deletion errors from BWA

Question

[arghyakusumdas]

I am new in using BWA. I will appreciate if someone can let me know how to detect insertion and deletion errors using BWA?

[WouterDeCoster]

bwa is an aligner. For finding differences between your reads and the reference genome you need a variant caller after the alignment, e.g. GATK.

Answer 1

[Hussain Ather]

Look at some assembly approaches to finding indels. BWA finds short insertions and deletions but using a de novo assembler or similar approach might be better.

You can also check out GATK (https://www.ncbi.nlm.nih.gov/pubmed/21478889/) which has a pipeline for detecting indels. https://www.broadinstitute.org/files/shared/mpg/nextgen2011/nextgen2011_delangel.pdf