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Check out the documentation at BaseRecalibrator.
The documentation says "This walker is designed to work as the first pass in a two-pass processing step..." How is the second pass run?
The second step uses PrintReads. See this article for details:
Geraldine Van der Auwera, PhD
Just to report a small bug here.
The dbSNP vcf in hg19 bundle has header for both b37 and hg19. But the lengths for chrM are different.
BaseRecalibrator will report error using this dbSNP as knownSites. Removing the b37 header solved the problem.
Thanks for reporting this, but I just tested it and it doesn't generate any errors. Perhaps you are using the b37 reference and not hg19?
Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT