Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
variant analysis -calling
I am working with plants, and so cannot follow most of your human/cancer specific workflows etc.
Also my question is probably not GATK specifc, but I would be very grateful for any kind of answer. I have used BWA to align a set of reads and the contigs assembled from these reads (de novo). I have used samtools mpileup and GATK unifiedGenotyper on the aligned reads. This results for both in a list of ONLY SNPs, the same ones (aside of sensitivity).
I have also used the samtools steps on the aligned contigs, resulting in a list of ONLY indels.
I can clearly see both SNPs and indels in IGV, both looking at the reads or the contigs.
generally I see that reads are being used for variant calling, so is it "wrong" to use contigs? and why do I not get ANY indels in either tool's output when using reads? any ideas?