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To future visitors to this thread, the format that it wants appears to be: --resource:hapmap,known=false,training=true,truth=true,prior=15 /path/to/hapmap.sites.vcf The beta docs specify two different formats, neither of which worked for me, …
It looks like you've specified a directory as an input to the workflow (/ngs/projects/3_GATK4/test_local_data-processing). The problem stems from the fact that that directory also happens to be the location that you're executing the workflow from…
In GATK 4, the GenotypeGVCFs tool only takes a single sample as input so you need to call an additional tool -- CombineGVCFs -- and send the output, which is now a single file, to GenotypeGVCFs.
GATK 4 doesn't yet have the CombineVariants tool (as per this post). I just pointed to the GATK3 jar for that step only and it worked fine. Also for GATK4, --filterExpression is changed to --filter-expression and --filterName is changed to --filt…