User: Dave Carlson
Dave Carlson • 40
- Reputation:
- 40
- Status:
- New User
- Location:
- Stony Brook University, NY
- Last seen:
- 5 days, 14 hours ago
- Joined:
- 2 years, 5 months ago
- Email:
- d*******************@gmail.com
Posts by Dave Carlson
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... Here is what the GATK developers [say][1] about using the HaplotypeCaller Spark implementation:
> This tool DOES NOT match the output of HaplotypeCaller. * * It is
> still under development and should not be used for production work. *
> * For evaluation only. * * Use the non-spark Haploty ...
written 6 weeks ago by
Dave Carlson • 40
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... Fixed, thanks. :) ...
written 6 weeks ago by
Dave Carlson • 40
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... As far as I know, there is no "-nct" equivalent in GATK 4. For HaplotypeCaller, even the Spark implementation is not yet recommended for use. ...
written 6 weeks ago by
Dave Carlson • 40
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... Hi All,
I'm trying to call variants in a set of plant genome samples using a bwa mem followed by GATK's HaplotypeCaller. However, I'm running into a potential roadblock that I'm hoping to get advice on. These genomes are rich in transposable elements, and when I visualize the alignments with IGV, ...
written 9 months ago by
Dave Carlson • 40
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... Good question. I'm in the same boat. What did you end up deciding to do? ...
written 10 months ago by
Dave Carlson • 40
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... One way to look for positive selection between two sequences is to examine the abundance of synonymous and non-synonymous substitutions present. Under a scenario of neutral evolution (i.e., where selection on the sequence is weak or non-existent and genetic drift is likely the main evolutionary dri ...
written 12 months ago by
Dave Carlson • 40
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... Did you ever solve this problem? I'm encountering something similar and am hoping there are answers out there. ...
written 22 months ago by
Dave Carlson • 40
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... Thanks. I'm running it again, specifically writing stdout/stderr to file this time. Hopefully if things still don't work properly, I'll have more info this time. Appreciate the suggestions! ...
written 24 months ago by
Dave Carlson • 40
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... Good idea. I just ran RepeatModeler on a small subset of my data, and it worked properly, producing all the appropriate output files. ...
written 24 months ago by
Dave Carlson • 40
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... Hi All,
I am running RepeatModeler on a ~300 mb plant genome assembly to annotate transposable elements. The program successfully runs without error but it doesn't produce the "consensi.fa.classified" output file, and the "consensi.fa" file is empty. I find it highly unlikely that my genome assem ...
written 24 months ago by
Dave Carlson • 40
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