Amanda

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Username
Amanda
Location
North Carolina
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Location
North Carolina
Full Name
Amanda Hulse

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  • Well Sheila, I have no idea what has changed, but it appears that it is working now. Perhaps the admins have changed something on our server that was causing the issue. Thank you!!
  • You can see there is no issue with it to begin running, but nothing is being written to the file even though it has already passed the markers here in the head of the file. INFO 15:19:48,217 HelpFormatter - Date/Time: 2017/07/05 15:19:48INFO 15:1…
  • Hi Sheila, It appears that it is not recognizing any variants in my file using ValidateVariants - as it is reporting Successfully validated the input file. Checked 0 records with no failures.INFO 14:06:44,904 ProgressMeter - done …
  • Hi @shlee Thank you, I tried running that however am still getting errors. gatk -T VariantFiltration -R formated60.fa -V output_raw.vcf -o Filtered_test5_AF.vcf -selectType SNP --filterExpression "AF < 0.2 || AF > 0.8" --filterName…
  • Hi Sheila, I am still working on it. SetNmAndUqTags was able to fix the issue found with NM tags. There was one other problem that I was able to fix with base quality. Thank you! Amanda
  • Hi Sheila, It appears that NM tags are missing from the original file from CLC. Interestingly their output must have changed over workbench versions. I'm running through picard to SetNmAndUqTags and hopefully that will solve the problem. Do you hav…
  • Hi Sheila, Since I'm back on for another question, I just saw this response. Yes that is exactly what I was trying to do, but I obviously solved it and not sure how I did since it has been some time. If you have a suggestion I can try that if I ne…
  • Hi Sheila, I will try running through there, however the file has been processed identically to every other run. Exported BAM from CLC run through the process to ensure correct formation: http://gatkforums.broadinstitute.org/discussion/2909/howto-f…
  • PS - I know that I can do this in two steps and combine then sort the resulting output, but I would like to understand why and perhaps it's a bug that will not allow both filters to occur at the same time. Thank you!
  • Hello Sheila, Can you please clarify, will INFO field now be recalculated in both SelectVariants and VariantFiltration steps? Thank you for fixing this issue, I was just coming back to see if there was a way around it, so very happy to see that you …
  • It seems that VariantFiltration is not updating the INFO field when it is setting filtered GTs to no call, which is then causing issue downstream for SelectVariants. This appears to be a duplicate issue that was found and reported here: http://gatk…
  • Hi Everyone, It seems that I also am running into this same bug. I'm also trying to filter using AN, but it is not being recalculated as everyone else has mentioned. This seems like a giant oversight in the pipeline as it would be the only way to i…
  • Hi Geraldine, Please disregard, I found a typo that had been integrated somehow into a saved script that was causing the error. Thank you!
  • Has there been a change in the options for adding read groups? I am getting an error where it says it does not recognize the option RGID. Thank you!