Is your feature request related to a problem? Please describe.
To bring EAGER2 to feature parity with EAGER1, a crucial step is genotyping and the creation of VCF files. EAGER1 used GATK UnifiedGenotyper (UG) as default, but has since been deprecated by the Broad institute. Furthermore, licensing of versions of GATK containing UG does not allow distribution of source code by others.
Describe the solution you'd like
To reach parity, I suggest we set up a system in EAGER2 where the pipeline contains a process which downloads GATK 3.8 for you, if a e.g. --genotyper unifiedgenotyper flag is given. Then subsequent processes follows EAGER1.
This thread will serve as a some general notes/discussion regarding this.
Describe alternatives you've considered
Use a different genotyper. However HaplotyperCaller does de novo assembly around possible SNPS/INDELs and this will rarely work on low coverage aDNA; and I'm not aware of extensive use of other genotypers. Furthermore, bacterial work at MPI-SHH requires UG for the current workflow.
Is your feature request related to a problem? Please describe.
To bring EAGER2 to feature parity with EAGER1, a crucial step is genotyping and the creation of VCF files. EAGER1 used GATK UnifiedGenotyper (UG) as default, but has since been deprecated by the Broad institute. Furthermore, licensing of versions of GATK containing UG does not allow distribution of source code by others.
Describe the solution you'd like
To reach parity, I suggest we set up a system in EAGER2 where the pipeline contains a process which downloads GATK 3.8 for you, if a e.g.
--genotyper unifiedgenotyperflag is given. Then subsequent processes follows EAGER1.This thread will serve as a some general notes/discussion regarding this.
Describe alternatives you've considered
Use a different genotyper. However HaplotyperCaller does de novo assembly around possible SNPS/INDELs and this will rarely work on low coverage aDNA; and I'm not aware of extensive use of other genotypers. Furthermore, bacterial work at MPI-SHH requires UG for the current workflow.