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3. Why do I get ‘Badly formed genome unclippedLoc: Contig chrY given as location, but this contig isn't present in the Fasta sequence dictionary’ when running GetPileupSummaries?

Dear Pamela, Thank you so much for your suggestion! This solution works for me. Thanks!  

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• Ruiqiao Bai
• October 02, 2021 10:24
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3. Why do I get ‘Badly formed genome unclippedLoc: Contig chrY given as location, but this contig isn't present in the Fasta sequence dictionary’ when running GetPileupSummaries?

Thanks for your suggestion! I have tried to solve the problem by providing a reference to GetPileUpSummaries, but received the error 'A USER ERROR has occurred: Contig chrY not present in reads seq...

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• Ruiqiao Bai
• September 29, 2021 23:58
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3. Why do I get ‘Badly formed genome unclippedLoc: Contig chrY given as location, but this contig isn't present in the Fasta sequence dictionary’ when running GetPileupSummaries?

Hi Pamela, thanks for your help! Since the  'lifted_small_exac_common_3.hg19.vcf.gz' file is lifted over from hg38 to hg19 using the 'hg19.fa' file (via the tool LiftoverVcf), I have checked the co...

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• Ruiqiao Bai
• September 28, 2021 00:30
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3. Why do I get 'java.lang.IllegalArgumentException: Dictionary cannot have size zero' when using GetPileupSummaries?

Yes, it works! I cannot appreciate more for your help!

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• Ruiqiao Bai
• September 21, 2021 16:35
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3. Why do I get 'java.lang.IllegalArgumentException: Dictionary cannot have size zero' when using GetPileupSummaries?

Dear Genevieve,   Thank you so much for your help! I have created the .dict file using the following command: gatk CreateSequenceDictionary -R /gatk/my_data/wgs_processing_facilitating_data/hg19.fa...

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• Ruiqiao Bai
• September 21, 2021 05:22
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3. How do I call somatic mitochondrial variants?

Dear Pamela,   Thanks a lot for your answer!  

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• Ruiqiao Bai
• September 21, 2021 05:00
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3. Why do I get 'java.lang.IllegalArgumentException: Dictionary cannot have size zero' when using GetPileupSummaries?

Sure. Thanks for your help! I have tested  UpdateVCFSequenceDictionary by two commands to get two updated files, but it seems that neither of them could work. Specifically, the first command is : g...

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• Ruiqiao Bai
• September 16, 2021 03:03
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3. Why do I get 'java.lang.IllegalArgumentException: Dictionary cannot have size zero' when using GetPileupSummaries?

Dear Genevieve,   Sure, for lifted_small_exac_common_3.hg19.vcf.gz, the command I used is: gatk ValidateVariants -R /gatk/my_data/wgs_processing_facilitating_data/hg19.fa -V /gatk/my_data/wgs_proce...

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• Ruiqiao Bai
• September 14, 2021 01:50
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3. Why do I get 'java.lang.IllegalArgumentException: Dictionary cannot have size zero' when using GetPileupSummaries?

I think another piece of information I would like to add is that before running Mutect2, I have used AddOrReplaceReadGroups to solve the error 'MISSING_READ_GROUP' in the input to Mutect2. Since I ...

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• Ruiqiao Bai
• September 14, 2021 01:28
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3. Why do I get 'java.lang.IllegalArgumentException: Dictionary cannot have size zero' when using GetPileupSummaries?

Dear Genevieve, Thanks for your reply! Both VCF files I used are not of size 0, and I have used ValidateVariants to check the two VCF files I used. For unfiltered_LP6005115-DNA_B07.vcf, the command...

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• Ruiqiao Bai
• September 14, 2021 01:14
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