Question

SNP analysis of genes

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9.5 years ago

sharma_tina189059 ▴ 50

Hi

Can anyone help in SNP analysis. Which online tool should I use to get the data for SNP.

snp • 3.0k views

ADD COMMENT • link updated 2.0 years ago by Ram 44k • written 9.5 years ago by sharma_tina189059 ▴ 50

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Do you mean online, like downloadable of something that can run completely in a web-browser environment?

Do you have a reference or not?

Are your reads cleaned up already or do you have raw reads, because those might need quality trimming...

Do you just want a VCF file with SNPs or do you want a genotyping output?

Please explain a little bit more about what you want and I can probably help a little bit (although I'm not an expert, I have only done SNP calling a couple of times)

ADD REPLY • link updated 2.0 years ago by Ram 44k • written 9.5 years ago by Lesley Sitter ▴ 610

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yes I have a reference seq. and i have got significant hits of query with ref. genome, then what about further analysis?

ADD REPLY • link 9.4 years ago by sharma_tina189059 ▴ 50

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You need to be more specific. "further analysis" could mean infinite tasks.

ADD REPLY • link updated 2.1 years ago by Ram 44k • written 9.4 years ago by karl.stamm 4.1k

Ram · Accepted Answer · 2015-07-20

Owhkee, so you did something like create a bowtie database (or bwa or whatever mapper you used), then aligned your reads or query against your indexed reference. Then you piped that to a Sam or Bam file right?

Well now you can do SNP calling, there are a lot of tools, i use Freebayes but I have also used Samtools Mpileup and BCFtools to get SNPs but for me freebayes works the best.

If you have more specific questions just aks, but i would first just read a little about SNP calling tools so you know for sure that you have the right tool for your project. And read the manuals to understand what the tools do. For freebayes you can look at this tutorial.