Bhanu Gandham
Computational Scientist
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Recent activity by Bhanu Gandham Sort by recent activity-
Hi Mark Farman Sorry for the delay. We are looking into this and will get back to you shortly.
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Hi Tom Morrison We reproduce results on our end once we have exhausted all other options. Can you please provide the mate pairs alignments of the reads you think should be filtered out? As mentio...
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Serena Ferraresso This is weird. This issue is almost always resolved by recreating the fasta file. As mentioned by you earlier, maybe this issue is because of the old version of samtools you are...
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Hi Tom Morrison I have a couple of suggestions for you to try, Can you please try to run it with MarkDuplicates instead of MarkDuplicatesSpark and see if that makes any difference? Try to run the...
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HI ABours Thank you so much for your input!
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Hi , The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlo...
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Hi Linda Do You don't need to worry about warnings. They do not effect your analysis or results. It's just giving you more information on what's going on under the hood. If you want more info on ...
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Hi Amit Can you tell me if the datasources are copied to each node or if they're on one central copy that all nodes are trying to access? It seems to be hanging on where it's trying to...
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Hi mk We would like to debug this issue on our end. Can you please share the original bam? We think that maybe, regardless of -use-filtered-reads-for-annotations some filtered reads contribute...
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Hi janrehker We finally found the bug!!! Thank you for your patience:) We are working on it and you can follow its progress here: https://github.com/broadinstitute/gatk/issues/6686 Thanks for bri...