The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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?