Hi all, I'm wondering which tools people are using for Illumina whole genome indel calling. I'm specifically interested in finding indels that are shorter than a read length. While we use other tools for somatic (tumour-normal) calling, what I'm most interested in here are tools that work on just one sample at a time.
Currently we are using Samtools mpileup to generate the SNPs and INDELS all at once. What other tools should I consider?