The documentation erroneously reported that AWS S3 buckets and Google Cloud Storage objects could be used as input or output for several tools.
Fix a regular expression escape character bug in bamtagger.
Fixed how the reference type is determined for human_par.
In mutect2 if the tumor and normal BAM files had the same PU value the output VCF would be empty. Fixed this by adding prefix "tm_" to tumor PU and "nm_" to normal PU and differentiate them.
licenseinfo for Flexera licenses no longer requires a GPU to function.
vcfqcbybam could generate an incorrect mapping quality score.