Ruiqiao Bai
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Activity overview
Latest activity by Ruiqiao Bai-
Ruiqiao Bai commented,
Dear Pamela, Thank you so much for your suggestion! This solution works for me. Thanks!
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Ruiqiao Bai commented,
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 commented,
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 created a post,
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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Ruiqiao Bai commented,
Yes, it works! I cannot appreciate more for your help!
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Ruiqiao Bai commented,
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 commented,
Dear Pamela, Thanks a lot for your answer!
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Ruiqiao Bai commented,
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 created a post,
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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Ruiqiao Bai commented,
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...