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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.