Given an alignment file (e.g. SAM, BAM), has anyone come across a tool that can create the equivalent of a sequence logo plot that also includes indels? Or, similarly, a tool to generate a position frequency matrix that includes indels?
My goal is to illustrate how a set of reads relates to the reference genome in aggregate over a given region.
I'm imagining a hybrid of Samtools Tview (e.g. below) and sequence logo plots such that insertions and deletions in multiple reads are collapsed and represented by frequency.
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Charles-Alexandre Roy •
1 answer
Most logo programs work without displaying indels. However, it may work if you can extract the alignment from this region and make a hidden Markov model (HMM) from it. There are tools to model indels in HMMs.
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you could combine a sequence logo with a splice graph but there's nothing about either of them that allows you to relate neighboring positions with each other