Best tool to find gene variants in metagenome data

vsnishtala · 08-23-2017, 04:52 AM

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 · 08-23-2017, 10:52 AM

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 · 08-24-2017, 03:34 PM

Quote:

Originally Posted by 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.

Thank you Brain Bushnell i will look into it !

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Tool to find splice variants	alex_ander	RNA Sequencing	0	04-02-2017 11:29 PM
Tool for viral metagenome assembly with extremely low coverage?	Rammaria	Metagenomics	1	05-11-2015 07:06 PM
Is there a tool to find if the gene ends are covered by RNAseq reads?	capricy	Bioinformatics	2	03-09-2015 02:36 AM
[Tool] Oncofuse: prediction of driver gene fusions from NGS data	mikesh	Bioinformatics	31	11-24-2014 09:07 AM
Tools or ways to find out variants in RNA seq data ?????	swapnil2188	RNA Sequencing	4	02-06-2012 01:03 PM

08-23-2017, 04:52 AM	#1
vsnishtala Junior Member Location: Rostock Join Date: Jul 2017 Posts: 3	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.

08-23-2017, 10:52 AM	#2
Brian Bushnell Super Moderator Location: Walnut Creek, CA Join Date: Jan 2014 Posts: 2,707	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.