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Old 11-05-2018, 02:16 AM   #2
henry.wood
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Location: Leeds, UK

Join Date: Apr 2010
Posts: 63
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I had a problem like this a while back. If your tiled amplicons can be identified and separated form their start-end positions, you can split them into separate bam files. Varscan2 has the option of mutation calling from multiple input bam files, and works nicely on PCR products. You can't use the somatic mode, if you don't have the paired data, but it picks up the mutations fine. You just need to parse the output to see how many of your mutations are called in multiple amplicons.
Hope that helps. Follow up questions would need me to dig around in old code, so might take a bit longer.
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