Hi,
I have been using an old version of PicardTools for some time and I have only recently decided to move to GATK4, mostly due to the improvements in performance. Upon doing so I have noticed that --IGNORE_SEQUENCE has become a required argument (see Documentation), whereas it used to be entirely optional (see the old documentation). It does not make much sense to me that the user has to specify a sequence that will be ignored, is it some kind of error?
Besides, the description of the option is truncated: "If a read maps to a sequence specified with this option, all the bases in the read are counted as ignored bases. These reads are not counted as "
The previous text continued with "Default value: null. This option may be specified 0 or more times." -- but of course it was optional back then.
