Lily

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Lily
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  • Hi Sheila, I'm using GATK 3.2.2 I found a problem in the HC gVCF file. It contains a line full of @s in the middle. I don't know what caused it. it I'm currently re-running the GenotypeGVCFs to re-create this file with the same sample list. I ho…
  • Hi, I run GenotypeGVCFs with 3.2 version, and it looks good :-) Here is the newer output for the same example as above: chr15 82637079 . C T 91046.53 . AC=26;AF=0.867;AN=30;BaseQRankSum=-1.146e+00;Clipp…
  • Hi Sheila, Sure I can share a snippet of the data, but, just to understand: What is better to use in order to merge the gVCFs files after HC and before VQSR: GenotypeGVCFs or CombineGVCFs? I haven't tried yet the GenotypeGVCFs in 3.2 version...…
  • I used GenotypeGVCFs I did it as it was suggested in previous question I asked: " you will run HC on your samples individually to generate GVCFs, then run all your GVCFs through GenotypeGVCFs together. This will produce a multi-sample VCF that you …
  • Hi Geraldine, Thank you - I followed the above and it works fine. However, I want to query about the recommended practice: In my routine work, I will get few additional samples from time to time, Is there a way to add samples to an existing mul…
  • Hi Sheila, Thank you very much for your answer. The link for the Variant Filtration was really clear and helpful. I still have a question about the Variant Recalibrator - and I apologize if it appears in the tutorial - I couldn't find a clea…
  • Thanks for the very prompt reply. You were right, it was just a typo... Thanks!! I hope it is OK that I'll take this opportunity to ask one more question: In the log followed the RealignerTargetCreator, I got the following messages: INFO 15:14…