Bhanu Gandham
GATK Forum Lead
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Activity overview
Latest activity by Bhanu Gandham-
Bhanu Gandham commented,
Tatiana Almeida Please search for this error message on google, this issue has been resolved in this forum and others multiple times. Searching for error messages in this forum and google first is ...
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Bhanu Gandham commented,
Good to know you were able to solve the issue and thanks for posting the solution!
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Bhanu Gandham commented,
Hi Patrícia H. Brito Are you on a shared NFS? How much physical memory do you have on your machine? I suspect that the tool is running out of memory which is why it is behaving this way. Can you a...
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Bhanu Gandham commented,
That's good! Good to know that using the reference solves the problem. It is possible that the tool requires some information not available in the bam file and hence providing a reference solves th...
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Bhanu Gandham commented,
Hi Patrícia H. Brito That an interesting problem. Can you run SelectVariants to convert the genomicsdb to a vcf and see if all the samples are present in the vcf. You could do this on a subset of...
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Bhanu Gandham commented,
zhaol Seems to me that there is still an issue with the new bam file. Can you please try these suggestion: You mentioned you fixed the bam, how did you do that? Please run validateSamFile on the c...
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Bhanu Gandham commented,
woodword Thank you so much for jumping in and helping the GATK community by contributing to the information we provide to the community through this forum!!
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Bhanu Gandham commented,
Hi Yangyxt I am not sure I understand your question entirely. If the question is whether or not GenomicsDBImport can write to multiple repos, the answer is not. It can add new samples to an exist...
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Bhanu Gandham commented,
Hi, Another user had a similar issue, take a look at this thread: https://gatk.broadinstitute.org/hc/en-us/community/posts/360057988172-CreateSomaticPanelOfNormals-fails- In fact this error has...
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Bhanu Gandham commented,
Manuela Bonetto You see this error when there is an issue with the input vcfs. Please post the content of GATK4teste_cohort.sample_map.txt. Please run ValidateVariants to validate your input vcf(B...