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Old 04-03-2020, 08:40 AM   #245
AndrewP
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Location: Boston

Join Date: Mar 2019
Posts: 11
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I'm trying to use BBmap to find all perfect hits or hits with an indel length 1.


Code:
bbmapskinner.sh  in=kmer.fasta out=result.sam ambiguous=all strictmaxindel=1
I'm running a control experiment where I have a subsequence to a larger sequence in the reference. I can find the subsequence in the reference if it's an exact match. However, if I add an indel in either the subsequence or reference, BBmap is unable to map the reference. I thought by setting strictmaxindel to 1, it should be able to report an alignment with a single indel. I've tried setting strictmaxindel to 10 and it still doesn't find the alignment.

Is there something that I am doing wrong?
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