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3. Masked reference genomes

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)
• August 16, 2023 08:55
• 1 vote

1. Technical Documentation
2. Algorithms
3. Evaluating the quality of a germline short variant callset

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)
• February 10, 2023 13:43
• 0 votes

1. Tool Index
2. 4.1.3.0
3. CollectHsMetrics (Picard)

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)
• January 17, 2023 13:13
• Edited
• 0 votes

1. Community
2. Other
3. Does GATK4 BaseRecalibrator not understand relative paths?

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)
• November 15, 2022 20:31
• Edited
• 0 votes

1. Community
2. Other
3. Does GATK4 BaseRecalibrator not understand relative paths?

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)
• November 12, 2022 08:52
• Edited
• 1 vote

1. Community
2. Other
3. Does GATK4 BaseRecalibrator not understand relative paths?

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)
• November 04, 2022 17:45
• 0 votes