Pipeline for creating a SNP dataset from scratch

Question

[anikcropscience]

Hello, I am a real bioinformatic noob. I have to start a project to make an SNP dataset from scratch. I have ~100 NGS sequencing datasets and a reference genome. My end goal is to create an SNP dataset for conducting genome-wide association mapping.

Can someone please give me a link or reference or tutorial showing a step by step procedure for making an SNP dataset from raw NGS sequence data?

I know it is hard to find a perfect tutorial as there are many. But any suggestions will be much appreciated. I really have no experience in this field and do not know from where to start. Thank you.

[GenoMax]

I have to start a project to make an SNP dataset from scratch

Based on what you wrote below this is not where you want to start. Creating a SNP dataset from scratch will be a difficult task even for someone who has been doing informatics for a while. Here is one example of a tutorial that walks you though basics.

This is a set of video tutorials that looks comprehensive.

[anikcropscience]

Thank you very much for those two informative links. Yes, I can feel the difficulty level already.

Answer 1

[Arup Ghosh]

Depending upon organism the variant calling method will differ, it will be easy to suggest tutorials and publications if you mention the organism name.

[anikcropscience]

It is an haploid microorganism (Plant fungi)

[Kevin Blighe]

Hello, I am a real bioinformatic noob. I have to start a project to make an SNP dataset from scratch. I have ~100 NGS sequencing datasets and a reference genome.

Thrown straight into the deep end?- no support from your supervisor?

You should take a look through the documentation for the Genome Analysis ToolKit (GATK). Unfortunately, nobody here has the time to take you through this step-by-step over a protracted period of time and deal with all issues that arise. If you need that level of help, then you should contract out the service.

[anikcropscience]

Not actually thrown, I will get help later on. But I want to try out myself first. As there are quite a few approaches and tools, I was not sure which one to use. That is why I asked for some tutorials. I do not expect anyone to teach me to step by step procedure. I was trying to get some links for tutorials which are common for beginners. Sorry, if I did not make it clear.

[Kevin Blighe]

کوئی مسئلہ نہیں / No problem / Sem problema / Sin problema / Senza problemi

[Arup Ghosh]

Check the Snippy pipeline: https://github.com/tseemann/snippy

Tutorial by galaxy team: https://galaxyproject.github.io/training-material/topics/variant-analysis/tutorials/microbial-variants/tutorial.html

[anikcropscience]

Thanks a lot. I will check those.