[svtoolkit-help] GenomeStrip Error Invalid Interval HLA-A*01:01:01:01 SVPreprocess

[mschwarz <m.s...@me...>]

Hi,

i try to run the lattest version of SVtools with the lattest 
reference/mask for HG38 from your server. When I start the 
SVPreprocessing script I get the following error:

java.lang.IllegalArgumentException: Invalid Interval HLA-A*01:01:01:01

It seems that the SVPreprocess-Script have problems with the additional 
contigs in HG38.

I try a workaround with the -L interval.list argument but struggle into 
an other error latter in the script.
(java.lang.RuntimeException: Unrecognized sequence: intervals.list)

Install-Test runs fine.

Hope you can help me.

Thanks

Martin Schwarz