WVNicholson
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Activity overview
Latest activity by WVNicholson-
WVNicholson created a post,
Question about using CNNScoreVariants, etc with targeted sequencing data
I'm interested in using CNNScoreVariants, etc with some targeted sequencing data (human data on 63 genes from about 400 samples) since the documentation says VQSR is not suitable for this and sugge...
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WVNicholson commented,
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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WVNicholson commented,
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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WVNicholson created a post,
Getting CNNScoreVariants to run faster
I was wondering if anything can be done to get CNNScoreVariants to run faster. There doesn't seem to be a Spark version of it yet. The documentation mentions the arguments "--inter-op-threads" an...
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WVNicholson created a post,
Recent research papers on current GATK
I was wondering if there are any recent research papers on current GATK, ideally peer-reviewed (but not necessarily) and from the team at the Broad Institute? I realise this is supposed to be cove...
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WVNicholson commented,
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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WVNicholson commented,
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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WVNicholson commented,
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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WVNicholson commented,
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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WVNicholson commented,
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...