Bhanu Gandham
Computational Scientist
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Recent activity by Bhanu Gandham Sort by recent activity-
Tim Bishop Looks like the somatic-hg38_1000g_pon.hg38.vcf.gz file is malformed. How was this file generated? Can you run ValidateVariants following the directions provided here to help identify the...
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Stephen Johnson Yeah looks like combining the bam files is the reason why you are seeing this error. Other users have faced similar errors. Here are a couple of proposed solutions: https://www.bio...
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Can you please post the new error log.
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zdr j Your germline resource and panel of normals is based on hg38 while your reference is hs37d5. I believe that is where this error is coming from. Please try again with the hg38 reference prov...
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Hi Tim, you are using a very old version of GATK which we do not support anymore. Could you try running with the latest version, 4.1.9.0
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Hi Prasun, Analyze Covariates is still part of GATK, here is the latest version: https://gatk.broadinstitute.org/hc/en-us/articles/360051304351-AnalyzeCovariates
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I also recommend going through and using these prebuilt workflows: https://app.terra.bio/#workspaces/help-gatk/GATK4-Germline-Preprocessing-VariantCalling-JointCallingMore info on how to use Terra ...
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Yangyxt I suggest rerunning the workflow without changing the gvcf files as mentioned here: I run HC on each contig and gather them to one using GatherVcfs in GATK and since the ##GVCFBlock meta-l...
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ISmolicz The the contamination.table and segments.table are usable. In the event of an error making them unusable the tool will throw an error and/or it will not generate an output. You don't need ...
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Official comment Hi Jyotsana Mehra 1. The fastest way to find what you are looking for is to look in our documentation first. We have generated an extensive list of documentation to help the community and most of y...