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Old 08-23-2017, 03:52 AM   #1
vsnishtala
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Default Best tool to find gene variants in metagenome data

hey ,

I was wondering did some body know any tools to find gene variants in metagenome data? I know about the freebayes and GATK, but which one is ideal to use on metgenome data and are there any other tools or pipelines to follow.
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Old 08-23-2017, 09:52 AM   #2
Brian Bushnell
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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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Old 08-24-2017, 02:34 PM   #3
vsnishtala
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Quote:
Originally Posted by Brian Bushnell View Post
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.
Thank you Brain Bushnell i will look into it !
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