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Old 08-23-2017, 09:52 AM   #2
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
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I don't know what's best for metagenome variant-calling, but a couple of additional options are Samtools mpilup + bcftools, and BBMap's CallVariants. I wrote a suggested variant-calling pipeline in the BBMap page, at bbmap/pipelines/variantPipeline.sh, which gives an example of how to preprocess the data and call variants.
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