Target capture sequencing

Question

[gubrins]

Heys! First of all sorry if the question is to basic, but I'm new to bioinformatics. I'm working with target capture sequencing and I'm having some problems to get the coverage of my target genes. The first thing I did is to map my fastq files to my target fasta files with bwa, but I don't exactly know how to obtain a general result for all the fastq files. If I have to check them individually I'll not finish.

I know the question is quite simple, but I'm struggling, so any help is going to be more than welcome :)

Thanks in advance!

[GenoMax]

Even though you may be doing targeted capture it would make sense to align to the full genome. That gives you an idea if there was off-target capture (you hope there would be none or little).

I don't exactly know how to obtain a general result for all the fastq files.

What do you mean by that? You want to get a summary of results for all samples?

[gubrins]

So what do you suggest, to align them to the full genome and later to my target genes? Regarding your question, exactly! I would like to get a summary of all my results for all my samples, is that possible?

Thank you very much!

[igor]

There are many "results" that you can generate. I would start with GATK Best Practices where they describe the workflows in detail: https://gatk.broadinstitute.org/hc/en-us/sections/360007226651-Best-Practices-Workflows

[gubrins]

Thanks!! I'll have a look! :)