BWA-MEM PARAMETER TO DETECT MUTATION
Hey, I am working with bwa- 0.7.18, in my alignment file I have manually checked for presence of mutation(snp) which is not been picked up by bwa as it shows perfect mapping of 159bp read length. I am working with amplicon data. I have tried to make mismatch score stringent(-B 20 ) but it still isn't picking up that mutation. Can somebody suggest what parameters can I use to make it more sensitive to mutations?
Thanks!
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Pierre Lindenbaum
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Bhawna •
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Bhawna •
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Can you show your evidence for this mutation?
show us the CIGAR string and the NM tag