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GATK 1.6 claims to apply a fixed Q20 threshold to clip ends of the reads for the indel caller:
3. 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.
--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
quality so that bases on reads with low mapping quality may get
filtered out depending on this value. Note too that this argument is
ignored in indel calling. In indel calling, low-quality ends of reads
are clipped off (with fixed threshold of Q20).
Can this "fixed threshold of Q20" be changed to another value when running the Unified Genotyper?