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santayana

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santayana
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  • OK, I will test this out. Thank you for your feedback!
  • Hi Ami and Geraldine, 1) Yes, I am following the pipeline that you have set out here, with the only exception of substituting HC for UG. 2) Ah OK, I understand now this is SplitNCigarString issue. I'll try changing the default option - thanks! 3) T…
  • Hi Geraldine, Thank you for your reply. It may be a moot point now, but please let me follow up your comment about HC vs UG for tumour samples, since this is a point of confusion for my colleagues and I. UG seems to me to be more suitable than HC…
  • https://drive.google.com/file/d/0B4VAqfRxlxGpYU0wX2xEdEQ0d1U/view?pli=1
  • (Image) Thanks for the quick reply Ami. The top window is whole exome and the bottom window is RNAseq from the same individual. It seems that the variant is only present in reads that only extend a few bases into the intron, suggesting to me tha…
  • Hi there, New member here. I was wondering whether you would consider adding your "dangling-head" functionality to the Unified Genotyper as well. I've decided to use UG for RNAseq variant calling because my samples are heterogeneous pri…