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pysam==0.7.5 is no longer available on pypi. Is the strict dependency still in place in 188.8.131.52? I would suppose much has changed since 2014.
I have the same error as Alessandro, and I did use the same reference for alignment and mutect. Since mine was run with a different version of the GATK, but I won't clutter with a dump unless it would help, since it looks very similar. Is there any …