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Indel Realigner using SNPs

I was just wondering, would it not be benefitial to use a database of SNPs togheter with the indels database during the indel Realigner step? I can be wrong, but it makes sense to me that knowing the location of the SNPs would facilitate the indel realignment step...

Thank you


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    I think the team has found that inputting a SNPs resource file will not help much after inputting the indels resource files. If you would like, you can certainly use both resource files as input.

    Please note, if you are using HaplotypeCaller or Mutect2 which do local re-assembly, you do not have to use Indel Realignment anymore. Have a look at this article for more information.


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