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Old 01-15-2018, 01:40 PM   #1
roliwilhelm
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Location: Ithaca, NY

Join Date: Jun 2012
Posts: 37
Default Calling Ambiguous Bases with Read Mapping

Hi There,

I've used MeGAMerge to merge two assemblies of the same data (https://github.com/LANL-Bioinformatics/MeGAMerge), but merging has produced many ambiguous bases. I have good read coverage, so I'd like to use read mapping to call the ambiguous bases (likely SNPs) based on majority rules. Can someone recommend a strategy for this? I've written a script to identify the location of all ambiguous bases and use 'samtools view' to grab all the reads that map to that location, and I could write a script to parse those reads at that specific position, but I hesitate because I'm sure someone has already solved this problem.

p.s. I've use pilon's fix '--amb' function, which should have done the trick, but the output is identical to my input. (https://github.com/broadinstitute/pilon/wiki)

Thanks in advance,
Roli
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