Matthew Miller

Member since January 23, 2020 17:03

Total activity 10

Last activity January 27, 2020 23:21

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Activity overview

Latest activity by Matthew Miller

Matthew Miller commented, January 27, 2020 23:21
Jason: You are so correct. I only looked at the header of the file (the part that is the SAM file style header) and didn't look at the bottom, interval section of that file. And I didn't realize...
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- January 27, 2020 23:21
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Matthew Miller commented, January 25, 2020 17:40
Ok. So I have it running. But it didn't spark the run across multiple intervals. Instead only one interval is running. I guess I don't really understand what is going on. In your system, you have ...
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- January 25, 2020 17:40
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Matthew Miller commented, January 25, 2020 17:18
Yes, I do need to create a new interval file, as I am not using a human genome. I am hoping that at least some of the terra workflows will work on non-model organisms. There are a lot of us that wa...
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- January 25, 2020 17:18
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Matthew Miller commented, January 24, 2020 16:08
Ok. I found how to access the file (a google cloud tutorial video would help us noobs). So if I understand correctly, in the workflow, I would generate a file in a google bucket that simply points ...
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- January 24, 2020 16:08
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Matthew Miller commented, January 24, 2020 15:57
Jason: Thank you for your help. How do I navigate to gs://gatk-test-data/intervals/hg38_wgs_scattered_calling_intervals.txt ? There doesn't seem to be any way to access it.
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- January 24, 2020 15:57
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Matthew Miller commented, January 23, 2020 18:11
Jason: I accidentally responded to a different post. I made one interval list as a hand made list. It runs fine locally on my computer with the -L flag. Here is the contents of the GATK-style list...
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- January 23, 2020 18:11
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Matthew Miller commented, January 23, 2020 17:16
Jason: I'm totally new to Terra. The workspace is "test". There are three submissions. All failed. But take a look at 157ddecb-0614-4458-8769-79a2a5d13290, because that one used the intervals fro...
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- January 23, 2020 17:16
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Matthew Miller created a post, January 23, 2020 17:03
Interval problem with haplotypecaller-gvcf-gatk4 (suggested workflow

I am trying to run the Suggested Workflow: haplotypecaller-gvcf-gatk4 I have created an interval list using the Picard ScatterIntervalsByNs tool. However, when I try to run the Workflow I get an er...
- Matthew Miller
- January 23, 2020 17:03
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- 11 comments
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Interval problem with haplotypecaller-gvcf-gatk4 (suggested workflow