WVNicholson
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Recent activity by WVNicholson Sort by recent activity-
The long run time on Terra seems to be due to a particular issue with Terra and/ or Google Cloud at the time. When I eventually got the example from the tutorial to run on my laptop, it actually j...
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I'm running into this problem as well. I'm not sure where gatkcondaenv.yml stands since I installed GATK4 with "conda install gatk4" from within my conda environment i.e. I didn't download a tar f...
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Although a very comprehensive manual page, I've voted as unhelpful because the dead links which were posted about a week ago and the lack of a contact e-mail address to report the problem.
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I'm not really clear from the above text if VariantRecalibrator and ApplyRecalibration are used in conjunction with CNNScoreVariants or if these are alternatives to one another. The text appears t...
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It's looking like using GATK v.4.1.4.1 is a workaround for me despite what I said earlier. (I guess previously Sue John meant v.4.1.4.0 specifically by v.4.1.4.)
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I believe I neglected to include the BED file used in the command line I provided. I don't have the file handy right now as I'm at home; but I'm fairly sure it had a single genomic interval 1:1535...
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Okay, I just posted the archive file - haplotypecaller_ec0942_bug_report_11mar20.zip - with the bug report. This has the smaller BAM file that reproduces the error from my last post. Hopefully th...
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Okay, I've been able to make a smaller BAM file that reproduces the error. It appears that neither of the reads in the original BAM file with the same QNAME have the same cigar string as in the er...
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Okay I have tried running HaplotypeCaller on the original BAM file now. Earlier I posted prematurely that it looked like it does not get the above error; but the job hadn't finished which obviousl...
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There's a medical confidentiality issue with the BAM file; so I will have to send an "excerpted" version of it, after confirming that I can reproduce the problem with that - depending on the bug an...