Hello,
When using LeftAlignandTrim with GATK 3.6 I have run into the problem that the INFO field of split fields is not preserved. Instead the info field for all the the new sites is ".". This then comes up as a downstream problem when I tried to use CatVariants (to reunite VCFs split by Chr) I get an error that "." is not defined in the VCF header. I saw in the release notes that there were changes to the tool specifically regarding the SMA flag. For the moment I will just use GATK 3.5 as a work around but wanted to bring this to attention.
James