GATK 1.6 claims to apply a Q20 threshold to clip ends of the reads for the indel caller:http://www.broadinstitute.org/gatk/guide/article?id=12373. Indel Calling with the Unified Genotyper
[...] while many of the parameters are common between indel and SNP calling, some parameters have different meaning or operate differently. For example, --min_base_quality_score has a fixed, well defined operation for SNPs (bases at a particular location with base quality lower than this threshold are ignored). However, indel calling is by definition delocalized and haplotype-based, so this parameter does not make sense. Instead, the indel caller will clip both ends of the reads if their quality is below a certain threshold (Q20), up to the point where there is a base in the read exceeding this threshold.Also here: http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_genotyper_UnifiedGenotyper.html
--min_base_quality_score / -mbq ( int with default value 17 ) Minimum base quality required to consider a base for calling. The minimum confidence needed in a given base for it to be used in variant calling. Note that the base quality of a base is capped by the mapping quali ...