James Emery
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Activity overview
Latest activity by James Emery-
James Emery commented,
Hi @Loïc Baerlocher. I notice that there might have been some confusion about the debug arguments that we posted based on your logs. Specifically both of the arguments `--debug-genotyper-output tru...
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James Emery commented,
Hello Pierre_Bioinfo. I will try to answer your all of your questions:First, why are the DP and AD values mismatching? We have an article that gets into some of the details here: https://gatk.broad...
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James Emery commented,
Hello Indrani Datta. Thank you for your interest. We have just updated the upcoming events page to include the hosting institutions and will update that going forwards.
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James Emery commented,
Hello Manikumar R. I'm sorry to hear about your issues with running the tool. The results you posted are not too unexpected since its entirely possible N regions or uncovered sections that are unma...
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James Emery commented,
If you are restricted to only running on one machine you might want to run the shards in series rather than in parallel. For normally behaved Illumina data 6GB + ~1-2GB overhead (the overhead is cr...
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James Emery commented,
Indrani Datta. You are going to have to check with each of the host institutions individually to look into ticketing/registration. There are recordings of some previous workshops available online i...
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James Emery commented,
Thanks SkyWarrior. I would add to your comment that the active region determination code in the HaplotypeCaller can have somewhat unexpected behavior when you are very close to the start of an inte...
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James Emery commented,
Hi Guido Vacano. Its difficult to tell what you mean. HaplotypeCaller can run out of memory for a number of reasons. Our general advice is to make sure the HC has ample memory available but crucial...
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James Emery commented,
Hello Indrani Datta. We have a list of upcoming workshops listed here: https://gatk.broadinstitute.org/hc/en-us/sections/360007134472-Events.
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James Emery commented,
In general if you are splitting it up by intervals you should do your best to put the interval boundaries between chromosomes or at hard to call/map or blocked out regions of the reference since th...