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 (Quote) But then, in the middle we have (Quote) According to the previous …
  • 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 point…
  • 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 oth…
  • 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 Cromw…
  • 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 it b…
  • 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 = 'A,TCC' …