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I understand that, but as I said there are no variants for the reference file, thus the VCF would be empty. Shall I skip the BQSR altogether or is there another way of re-mapping the reads that does not require a VCF file? Thanks
Looks like I can work with openJDK: I changed the default java version with: $ sudo update-alternatives --config java [sudo] password for : There are 2 choices for the alternative java (providing /usr/bin/java). Selection Path …
Thank you. Can I install multiple version of Java? Do I need to tell GATK what version it shall use with a particular flag? Can I use openJDK?