Include description of how to bypass FASTQ duplication check in error message.
Update pylint settings.
Old name used in message.
Improve validation of singleton filtering settings; prevent problems when a sample is filtered by its own group.
Document GenotypeEntirePrefix setting, default to realigned (like BAM pipeline).
Remove -k flag from gzip invocation

It is not required (files are temporary anyway), and is not supported by
all versions of gzip.