Best tool to find gene variants in metagenome data

[vsnishtala]

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.

[Brian Bushnell]

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.

[vsnishtala]

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 !