MESSAGE: Unable to create iterator for rod named variant in GenotypeGVCFs

boymin2020boymin2020 New YorkMember
edited August 2016 in Ask the GATK team

Hi all,

I tried everything I can do, but can not find the solution. Any help will be appreciated.

PROGRAM DETAILS:

GATK version: GATK v3.6-0-g89b7209

Program Args:
-T GenotypeGVCFs
-D dbsnp_137.b37.vcf -R human_g1k_v37.fasta
-L CHROM_1_1_.bed -V:VCF indi_1.list
-A AlleleBalance
-A BaseQuality RankSumTest
-A Coverage
-A HomopolymerRun
-A MappingQualityRankSumTest
-A MappingQualityZero
-A QualByDepth
-A RMSMappingQuality
-A SpanningDeletions
-A FisherStrand
-A InbreedingCoeff
--standard_min_confidence_threshold_for_calling 30
--standard_min_confidence_threshold_for_emitting 30
-o CHROM_1_1.joint.vcf

ERROR MESSAGE: Unable to create iterator for rod named variant

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