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Hello Genevieve, Thanks so much for the explanation. It's perfectly clear now. Best Jorge

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• jorgez
• June 21, 2021 20:09
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3. FixVcfHeader error: A reference dictionary is required for creating Tribble indices on the fly

Hi, Not on vcf files produced by either Platypus or VarScan. Jorge

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• jorgez
• July 21, 2020 14:38
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3. FixVcfHeader error: A reference dictionary is required for creating Tribble indices on the fly

Hi again, I did a bit of testing and confirmed that FixVcfHeader works on vcf files produced by GATK and SAMtools but it fails in vcf files produced by VarScan or Platypus. This is the behaviour I ...

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• jorgez
• July 21, 2020 10:25
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3. FixVcfHeader error: A reference dictionary is required for creating Tribble indices on the fly

Hi, This is the log for IndexFeatureFile (A) and FixVcfHeader (B) A:  IndexFeatureFile Using GATK jar /mnt/netapp1/Optcesga_FT2_RHEL7/easybuild-cesga/software/Core/gatk/4.1.7.0/gatk-package-4.1.7.0...

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• jorgez
• July 21, 2020 10:19
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3. FixVcfHeader error: A reference dictionary is required for creating Tribble indices on the fly

Hi, Yes, the index was created successfully with IndexFeatureFile

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• jorgez
• July 20, 2020 21:44
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3. FixVcfHeader error: A reference dictionary is required for creating Tribble indices on the fly

Hi, Both (A) the usual sort,  bgzip and tabix sequence followed by FixVcfHeader  or (B) or IndexFeatureFile followed by FixVcfHeader fails with the error 'A reference dictionary is required for cre...

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• jorgez
• July 20, 2020 21:10
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3. LiftoverVcf fails to lift over a GVCF file. Error java.lang.ArrayIndexOutOfBoundsException: -1

Hello Bhanu, This is my only one chain file: http://hgdownload.cse.ucsc.edu/goldenpath/hg38/liftOver/hg38ToHg19.over.chain.gz Jorge  

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• jorgez
• June 19, 2020 12:51
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3. LiftoverVcf fails to lift over a GVCF file. Error java.lang.ArrayIndexOutOfBoundsException: -1

Hello Bhanu, I am afraid the problem persists even lifting over to a reference conatining only autosomes, X, Y and M like this: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 ...

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• jorgez
• June 18, 2020 17:56
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3. LiftoverVcf fails to lift over a GVCF file. Error java.lang.ArrayIndexOutOfBoundsException: -1

Hello Bhanu, I have shared my dict file here:https://gist.github.com/jazberna1/4b4ca9cba42753c5ca884687574b2e05#file-hg19-dict These are the contig names in the dict file:https://gist.github.com/ja...

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• jorgez
• June 09, 2020 09:28
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3. LiftoverVcf fails to lift over a GVCF file. Error java.lang.ArrayIndexOutOfBoundsException: -1

Hello again Bhanu, I was missing get you the full log. There it is. Thanks so much  Jorge     Using GATK jar /mnt/netapp1/Optcesga_FT2_RHEL7/easybuild-cesga/software/Core/gatk/4.1.6.0/gatk-package-...

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• jorgez
• June 03, 2020 11:13
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