Bhanu Gandham
Computational Scientist
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Recent activity by Bhanu Gandham Sort by recent activity-
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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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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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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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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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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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...
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Please post the version of GATK you are using, the exact command and the entire error log.
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Kshama Aswath Thank you so much for sharing your GATK experience here. Your interactions and suggestions will help build the knowledge base of this forum and help other scientists with their rese...
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Yangyxt The Error suggests reducing the max-gaussians. Have you tried that? If not I would recommend doing that.
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masagis This question has been posted on the forum before, please take a look at the suggestion provided there: https://gatk.broadinstitute.org/hc/en-us/community/posts/360072673351-Error-Caused-...