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Old 12-12-2011, 07:48 PM   #1
Location: shanghai

Join Date: Nov 2010
Posts: 24
Default VariantAnnotator ReadPositionRankSumTest Error

my command:
java -Xmx20g -jar GenomeAnalysisTK-1.3-24-gc8b1c92/GenomeAnalysisTK.jar \
-T VariantAnnotator \
-R hg19fastadatabase/ucsc.hg19.fasta \
-I dedup_mate_recal.bam \
--variant recal_raw.vcf \
--dbsnp hg19_GATK1_1/dbsnp_132.hg19.vcf \
-o output2.vcf \
-A FisherStrand \
-A MappingQualityRankSumTest \
-A ReadPositionRankSumTest \
-A RMSMappingQuality \
-A MappingQualityZero \
-A QualByDepth \
-A HaplotypeScore \
-A DepthOfCoverage \
-A BaseQualityRankSumTest

I got the Error:
##### ERROR MESSAGE: Invalid command line: Argument annotation has a bad value: Class ReadPositionRankSumTest is not found; please check that you have specified the class name correctly
##### ERROR ------------------------------------------------------------------------------------------
ReadPositionRankSumTest (ReadPosRankSum)

how can i solve this problem
wanguan2000 is offline   Reply With Quote
Old 12-13-2011, 01:02 AM   #2
Junior Member
Location: A

Join Date: Sep 2011
Posts: 1

Hi there,

the correct name of the annotation is ReadPosRankSumTest.
Version GATK-1.2-4

msa is offline   Reply With Quote

readpositionranksumtest, variantannotator

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