santiagorevale

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santiagorevale
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  • Nevermind, I found the answer in the following link: https://github.com/gatk-workflows/gatk3-4-rnaseq-germline-snps-indels/issues/4 Thanks anyway.
  • Hi there, I hope you could help me unravelling this, because I always found confusing the definitions and examples for ID and PU. In the beginning of the document it says In the simple case where a single library preparation derived from…
  • Hi @shlee, Regarding to bundle, I was able to find it properly. However, I was unable to find any haplotype map file there. What I was asking is if maybe you are already using a file for this and would be able to share it as well. Thanks for p…
  • Hi @shlee, I don't understand much of population genomics. My goal in this case is to be able to identify which of the NGS samples corresponds to each array sample data. So, why do I need a population file as input for any of the tools? On the…
  • Hi there! Were you able to check any of the previous questions? Regarding question 2b) I was able to download the file, but I still would like to know how did you create it. Thanks in advance. Best regards, Santiago
  • Thanks for your comprehensive reply, Chris. I'll give it a try and come back to you if anything goes wrong. Cheers!
  • Hi Chris, Thanks for your quick reply! Would just setting up the options under "SGE" be enough to start using Cromwell with that config file? Or is there any other option I should be setting from the file? Also, what is the aim of Cromwell'…
  • Thanks, Geraldine. So how would GATK classify this second example? Because it's not an MNP (it should be the same number of nucleotides) but it's more like a complex substitution. Is there a name for this type of complex substitutions? Should …
  • Hi Sheila, I'm still confused. When you talk about alleles in the above mention FAQ, what's the difference between MIXED and SYMBOLIC? Could you give me an example? Are these two examples correct? * MIXED: e.g. Reference = 'T', Sample …