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Method to include insertions in compact alignment from BioMap object?

Asked by Turner on 25 May 2013

Hi all,

I'm working with a BioMap object containing 50bp sequencing reads from a BAM file. My goal is to retrieve a full genome sequence from the BioMap. So far, I know how to use getCompactAlignment to get a memory-friendly version of an alignment that can be converted into a consensus sequence. I've mastered how to handle deletions, but getCompactAlignment does not account for insertions, and actually removes them from the alignment. Is there another method to generate a compact alignment or direct consensus sequence from a BioMap that includes insertions?

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Turner

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