I've been establishing my own first pipeline for calling variants: Indels and SNPs. For that, I used mainly GATK tools.
I'm doing this for whole genome and whole exome sequences of mouse inbred strains.
So I'd like to hear your opinion about calling Indels with SomaticIndelDetector (--unpaired flag for simple sample) or UnifiedGenotyper (INDEL mode).
Which one gives better results and is more appropriate for my study?