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nanjalaruth / hla_typing_using_HLA-LA

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Debugging HLA-LA #1

Open nanjalaruth opened 1 year ago

nanjalaruth commented 1 year ago

Errors you might encounter and solutions.

  1. Have found no compatible reference specifications. https://github.com/DiltheyLab/HLA-LA/issues/61
  2. Picard not found. The solution is to download the jar file from the attached site and add path to a file called "paths.ini"https://sourceforge.net/projects/picard/files/picard-tools/1.119/
  3. Failed to populate reference error. https://github.com/samtools/htslib/issues/950
  4. Failed to read the header [-]. The solution is to use Samtools version 1.6 and above
  5. If downloading Boost manually, follow the steps on the main pagehere
dennis-serum commented 1 year ago

I am having the problem with the compatible reference (item 1 above). However, from issue #61 I still don't see how to fix it. Would it be possible to add this fix to the readme?

nanjalaruth commented 1 year ago

Hi Dennis, did you download "https://github.com/DiltheyLab/HLA-LA/files/7252781/reference_extraction_UNIX.txt" file?

dennis-serum commented 1 year ago

Thank you for the reply. I think that each user needs to generate this for their own bam file input. However, I did try that specific file and it did not work. Is running samtools idx on your bam enough? What modifications does the output need?

nanjalaruth commented 1 year ago

I used the same file and it worked for me. I am not sure about samtools idx. Maybe try it?