Question

Software to predict impact of SNPs or Indels

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5.3 years ago

williamsbrian5064 ▴ 510

Hi,

I work with nonhuman data. I have a bunch of SNPs that I want to predict how deleterious the SNP is. I know there is software out there like sift, polyphen, and provean. The issue I have is that you have to manually input them. I was wondering if anyone has developed a pipeline to mass submit SNP?

I know you can download polyphen and provean but you have to make a .fasta file and file with the SNPs of interest for every protein. I just don't want to do that for thousands of SNPs

I know Sift is a bit better. You can just run an entire VCF and it will give you predictions for everything at one. However, I think Sift isn't the most accurate.

Does anyone use any other software? or does anyone do something different to predict the effect of SNP a protein?

Thanks!!

SNP genome next-gen • 1.5k views

ADD COMMENT • link 5.3 years ago by williamsbrian5064 ▴ 510

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...are you in the same bioinformatics course as this guy? - How to choose good tools for identifying functional SNPs?

ADD REPLY • link 5.3 years ago by Kevin Blighe 87k

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Hahaha no. Just a frustrated grad student. Kevin, you the bomb. You never disappoint.

ADD REPLY • link 5.3 years ago by williamsbrian5064 ▴ 510

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Can you mass submit for any of those?

ADD REPLY • link 5.3 years ago by williamsbrian5064 ▴ 510

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Yes, you can bulk query against most of those. Most are available as VCF/BED files as they are essentially annotations tied to a chromosomal position.

ADD REPLY • link 5.3 years ago by Ram 43k

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Very cool! Any favorites that you prefer? I am running into some that are available for humans :/

ADD REPLY • link 5.3 years ago by williamsbrian5064 ▴ 510

score 3 · Accepted Answer · 2018-12-17

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5.3 years ago

Ram 43k

From your question you seem to be really opinionated on SIFT. I think SIFT and PolyPhen2 are pretty standard and the way to go. Most sites allow you to upload a file, so you should be fine, unless you need to run more than the allowed volume, at which point you're better off using ANNOVAR.

ADD COMMENT • link 5.3 years ago by Ram 43k

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I was really just listing sift and polyphen. I like sift because you can download the software and it will run an entire VCF file with no other input. Polyphen2, you have to do a lot of manual labor. I would like to find 2 or 3 different software that I can just upload my VCF and go. Maybe that is ANNOVAR? I will check it out. I only ask because my VCF file is HUGE

ADD REPLY • link 5.3 years ago by williamsbrian5064 ▴ 510

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I only ask because my VCF file is HUGE

Then a local tool install is the way to go for practical reasons of getting timeouts etc with uploads.

ADD REPLY • link 5.3 years ago by GenoMax 141k

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Yeah! I am on the prowl for some right now. Do you have any preferred software?

ADD REPLY • link 5.3 years ago by williamsbrian5064 ▴ 510

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You're going in circles. The question has already been answered; there is no easier way to annotate a VCF. You should really read Kevin's comprehensive answer on the linked post, it along with jared.andrews07's comment on it and my answer here address everything you'll need.

ADD REPLY • link 5.3 years ago by Ram 43k

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That hurt my feelings a little bit

ADD REPLY • link 5.3 years ago by williamsbrian5064 ▴ 510

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This is a professional forum run entirely by volunteers, and we need to strike a balance between being a pure knowledge repository and a Q&A forum. When a conversation meanders into personal preferences and repeated discussions on well-established practices, it needs to be discouraged.

You're welcome on biostars slack if you'd like to interact with us in a more informal setting, but that is no guarantee that an ad nauseam discussion will be indulged.