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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?

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