I've been asked to design an easy-to-use SNP caller at work (presumably for staff who don't know how to use a linux environment and would like the avoid the hassle of such). I've gone about doing this with some fairly traditional tools: bowtie2 for alignment, samtools and bcftools to modify sam files and generate pileups, SNVer for variant calling, etc.
And then I started reading about platforms like GATK that already do this, and thought that it might be better to investigate that as an option instead.
So, now I'm wondering: for those of you who have used GATK, do you prefer it to more 'traditional' alignment and variant calling methods (i.e., ones where you've written and customized most of the script yourself)? Are there any drawbacks to GATK that I should be aware of before investigating it as a primary alignment+variant calling tool? (I realize that GATK works primarily on a linux env, but I shouldn't have a problem creating an external GUI to be able to control some of its features.)
Any feedback would be great! Thank you.