identifying aspecific snp in sequenced genes

Question

[tariktj]

Hi all,

Having a set of sequenced genes in a file in fastq format, are there any tools that can check if a specific snp (I have the ID of this specific snp) is present in the sequenced genes ?

Thanks.

Answer 1

[DVA]

There are a few ways to do this. If you will eventually look at more SNP sites I would recommend you do a full variant calling pipeline. For example: 1. align the fastq raw reads to reference genome (you can use BWA-mem) 2. Remove duplications and sort using samtools and/or picard. 3. Call variants (e.g. using GATK) 4. Annotation and see if the expected SNP(s) is presented.

However, are you only interested in one single SNP? If so, you can just do step one - alignment, and download a genome visualization software such as IGV, and just zoom in to your SNP of interest and take a quick look.

[tariktj]

1- Thanks a lot, you've just put me on the track. Actually there are more than one snp. So I will read more about such pipelines to get a clearer idea, I guess they are called 'snp calling'?

2- and one more thing that I need to know from you please: so this whole process can be automated without the need for any visual intervention from the user, right ? I mean, the user will just run some scripts (that need to be developed) on the fastq file, and get an output report stating whether certain snps exist in the sequenced genes or not?

[DVA]

1. yes correct, also called variant calling
2. theoretically, yes. However, in practice, there are many things you have to pay attention when you get raw reads. For example, the quality of the reads - not all are worth processing (you can look into FastQC). Also, there are always more than one software to choose from, so you have to be sure the pipeline you use fits your purpose.