The most used resources are Galaxy (https://usegalaxy.org/) and GATK (https://gatk.broadinstitute.org/hc/en-us). I used Galaxy to perform SNP analysis on plant genomes, but the method should be similar for other organisms as well. Your data files are .bam/.vcf so I am assuming that it has already been trimmed and assembled. The remaining steps are listed below (along with helpful tools to accomplish each of the steps in Galaxy):

- SNP calling (Getting only the SNPs out of your NGS data): 'bcftools call'/'call variants'

- Filtering (Filtering out the unnecessary SNPs): 'SnpSift Filter'

- Comparing (between the control and the samples; finding out matches): 'bcftools isec'

- Annotating (figuring out the gene locus of the SNPs): 'SnpEff Eff'

There are many other tools that you can use as well. If you are stuck, browse through Galaxy and find other tools that may help to solve your problem. Read the documentation for more info.

Best of luck!

PLINK has very rich functionality, but command line interface makes it is very tricky indeed to select required arguments. The best source is the official site: https://www.cog-genomics.org/plink/1.9/

There you will find description of all arguments and how to use them. This particular page describes what you need:

https://www.cog-genomics.org/plink/1.9/assoc

Also pay attention to input section .

It's important that you take your VCF files and extract the important data out of it first. I have developed a tool to do so https://github.com/everestial/VCF-Simplify

You can then load the data on R or python; then develop/use the methods and statistics that fits the assumption of your data and kind of research you are doing.

Hello, everybody.

Can someone help me about the quality control process at Plink?

Best regards