multisample SNP calling in plants
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Entering edit mode
5.6 years ago
Covux ▴ 10

Hello,

I am beginning to working on a project that eventually should be able to do multi sample SNP calling in plants.

I am a novice in bioinformatics and never used any Linux or Python, that is something i am also currently learning on how to use software in a Linux environment and learn to use python. I did use software like UGENE in the past.

I have done SNP calling before but only on a small scale regarding a bacterium and this was a project i had to do for a course in college. that also how i eventually wanted to go into bioinformatics. My formal back ground i biomedical Sciences but i want to go more into bioinformatics instead of the lab.

Now for my project, I have so test one diploid plant and one polyploid plant.

the last days i have reading this website and been searching for all kinds of questions regarding multisample of single sample SNP calling. and SNP calling in general. I also have been looking for papers and looking for videos on youtube regarding this topic. This was all to get a more general idea of the topic and to see where in lack knowledge.

Some of the papers i have read( thanks to this website) are:

Systematic comparison of variant calling pipelines using goldstandard personal exome variantsSohyun

Validation and assessment of variant callingpipelines for next-generation sequencing

A Comparison of Variant Calling Pipelines Using Genome in a Bottle as a Reference

With reading all kinds of papers i did the last days i find one thing more difficult to find. and that is finding a paper that applies to plants instead of human or mammals.

before i make any further plans on what software to use of even how to use them i would like to find some information or papers that discus SNP calling (on a large scale) for plants.

Should i also start thinking already on how many haplotypes the plant has when i want to make a pipeline/work flow or using existing pipelines/work flows in for example galaxy. Or is that something i don't have worry about?

Maybe Someone here can point me in a good directing on where to start reading for SNP calling in Plants and if there are things i have to look out for compared to SNP calling to humans/mammels.

Maybe this story i a bit vague, if you have any questions i will be happy to answer them.

KInds regards Covux

SNP multisample • 2.0k views
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Entering edit mode

Hi Covux,

It would greatly increase the probability that someone posts a useful answer if you decide to use proper grammar, punctuation, and capitalization. As it stands, your post looks lazy, which deters people from reading it. It's good that you have done some research, but it's also helpful to put effort into your posts. For example, when referring to yourself, the letter "I" is capitalized. Also, the first letter in a sentence is capitalized.

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Brain,

Thank you for your remarks.

I know my grammar in English is really bad. I did spend an hour on this text and thought I fixed most things.

Thank you for pointing out my faults and correcting them.

Covux

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Entering edit mode
5.5 years ago

Hi, Covux!

You may try bcbio germline variant calling pipeline. Set it up, add custom reference genome, and call variants with GATK. (It supports up to 7 variant callers if you need that many).

Good luck!

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Entering edit mode

Thank you for the information!

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