Eva (Evander)
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Activity overview
Latest activity by Eva (Evander)-
Eva (Evander) commented,
Hi ah yeah, I did run that. It seemed ok to me, but I might have missed something. For completeness, this is what I did: - updated to gatk 4.5.0.0. Did not work, broke my other stuff- adjusted thre...
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Eva (Evander) created a post,
gatk CollectVariantCallingMetrics MultiThreadedChunkBased: Unexpected exception encountered in child thread. java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
I have run the same command on two other .vcf files from different variant callers (deepvariant and gatk), with the same reference genome, bed file/targets, and dbSNP file. They have no issues and ...
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Eva (Evander) commented,
Dear Derek Caetano-Anolles, thank you for this useful comparison. I just have a small question to clarify something I could not find in the above text or in the Clara Parabricks website. Were the v...
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Eva (Evander) commented,
Thank you for the great explanation! I have one comment and one question. The comments is that the link to the figure "The relationship between variant-level concordance and genotype concordance i...
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Eva (Evander) commented,
Dear GATK, Could I suggest a more concise section on what is filtered in the ouput of HSmetrics per target metrics? Because I was thoroughly confused about why I was not getting any coverage on som...
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Eva (Evander) created a post,
CollectGcBiasMetrics for Exome data
Dear GATK community, I want to see if there is any GC coverage bias in exome data. I am using CollectMultipleMetrics with the -PROGRAM CollectGcBiasMetrics. Is there any way to make the plot for ex...
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Eva (Evander) commented,
Hi Anthony, thanks for asking the developers. If that were true (although I do not think that it is practically…I tried), it still does not behave like this when running the tool. Because in the ca...
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Eva (Evander) commented,
Dear Anthony, sorry for the late reply. Thank you for answering. Yes, everything is there, and works if I do not use the relative paths pointing to the files. In other words, when I run the command...
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Eva (Evander) commented,
Hi Robert, When I run the command in the terminal with the relative path "../some_dir/path_to_file" (with the "../"), it does the same thing. It seems to append the relative path, as a string, to ...
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Eva (Evander) created a post,
Does GATK4 BaseRecalibrator not understand relative paths?
I am using GATK 4.2.6.1. and for some reason GATK BaseRecalibrator is not getting my (relative) paths. It pastes them to the path all the way up to the home directory (as you can see at the end of ...