
Ruiqiao Bai
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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! I am using GATK4, and I have successfully used the GetPileupSummaries tool to deal with the data of one subject in my dataset, following the tutorial of Mutect2 to call somatic variants. Howeve...
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How do I call somatic mitochondrial variants?
AnsweredHello! I am using GATK4 MUTECT2 for calling somatic variants from the whole genome sequencing dataset. I have noticed that MUTECT2 have a ‘mitochondria mode’ (https://gatk.broadinstitute.org/hc/en-...
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Why do I get 'java.lang.IllegalArgumentException: Dictionary cannot have size zero' when using GetPileupSummaries?
AnsweredHi! I am using GATK4 following the tutorial (How to) Call somatic mutations using GATK4 Mutect2 – GATK (broadinstitute.org) for detecting somatic variants. I have received an error when using GetPi...