How to detect insertion and deletion errors from BWA
I am new in using BWA. I will appreciate if someone can let me know how to detect insertion and deletion errors using BWA?
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Hussain Ather
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arghyakusumdas •
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arghyakusumdas •
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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
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