Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
DepthofCoverage, argument with name 'includeRefNSites' isn't defined?
I am trying to run a depth of coverage calculation as part of the XHMM workflow for cnv analysis. Upon running the following bash code, I am returned with this error.
java -Xmx3072m -jar ./Sting/dist/GenomeAnalysisTK.jar \
-T DepthOfCoverage -I group1.READS.bam.list -L EXOME.interval_list \
-R ./human_g1k_v37.fasta \
-dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable \
--minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 \
--countType COUNT_FRAGMENTS \
ERROR MESSAGE: Argument with name 'includeRefNSites' isn't defined.