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Including certain patches in the GATK resource bundle

vkulluvkullu San FranciscoMember

I noticed that the GATK resource bundle does not have all the patches from here (http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25/#/def_asm_PATCHES). I need to add a few like GL582971.1. This brings me to my question:
1. For the GL's included by default in the bundle what was their inclusion criterion?

  1. Do you have a resource bundle which has ALL the GL's as per the release notes on NCBI (above link)?

  2. If I were to add a few, what is the process you'd recommend?



Issue · Github
by Sheila

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  • SheilaSheila Broad InstituteMember, Broadie admin

    Hi Vinayak,

    I am not exactly sure about this. I will ask the developers and get back to you.


  • ebanksebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭

    I'm pretty sure that we use the official reference used by the 1000 Genomes Project.
    If you want to alter the reference, you can certainly do so. Just apply the patches and follow the instructions for regenerating the fasta index (.fai) and dictionary (.dict) files.

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