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Inconsistent handling of high base quality scores
It seems as if the handling of sam/bam/cram files with higher-than-usual base quality scores is inconsistent. In particular, a base quality score of 93 causes HaplotypeCaller to throw an exception if a bed file is supplied, but not if the target region is expressed in chr:start-end format. For instance, for the same bam file, invoking HaplotypeCaller like this:
-T HaplotypeCaller -R my-ref.fa -I alignment.bam -L my-bed-file.bed
returns an error regarding higher-than-expected base quality scores, but
-T HaplotypeCaller -R my-ref.fa -I alignment.bam -L chr1:500-1000
works just fine, even though the region in the bed file is identical to the region given as a command line arg.
Confusing and a little frustrating.