Ricky Magner
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Activity overview
Latest activity by Ricky Magner-
Ricky Magner commented,
I did take a look at the code, and it does seem like there's a step early on where the SM tag value is extracted from the RG and fed to a bunch of functions later on, most likely leading to your `n...
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Ricky Magner commented,
Hi, I'm still trying to test this a bit, but can you confirm: If you add a "SM" field to the RG line, does it produce the same error? What do you mean when you say it "works" when specifying the c...
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Ricky Magner commented,
Hi, thanks for posting. I tried recreating your issue with some of my own data but couldn't reproduce it. In particular, I used the same flags as you with a BAM I knew mismatched my VCF sample and ...
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Ricky Magner commented,
Hi, I think this depends a little bit on what you're trying to do, and what you hope to get out of "matching alleles." Here are two use cases I can imagine: 1. If you want a cohort of many samples ...
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Ricky Magner commented,
Hi, Could you elaborate a little bit on the "server's product queue error"? In particular, if there's a stacktrace you can share output from the tool, that would be very helpful in trying to debug ...
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Ricky Magner commented,
Hi, We typically only support technical questions regarding how to use our GATK software, but I'll try to give a few comments about your questions (other users are of course welcome to provide some...
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Ricky Magner commented,
Hi, Do you think you can provide an example for debugging purposes, of one line from the VCF and one line from the BAM file that contribute in an unexpected manner towards the count from ASEReadCou...
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Ricky Magner commented,
Hi Le, I spoke with someone who did an informal analysis internally who said they said modest improvements by following the DRAGEN filtering strategy, but VETS (the VQSR replacement) is also pretty...
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Ricky Magner commented,
Hi Le, On a technical level, the gVCFs produced by DRAGEN-GATK are still valid gVCFs produced by GATK, so they should pass through tools expecting that sort of input. I am not aware of any big stud...
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Ricky Magner commented,
Hi Akshay, Thanks for your post about this tool. As mentioned in the documentation, the tool currently only supports SNPs. It's possible that in the future the GATK team might consider extending fu...