How do I get known-SNP, Indel files in hg19 version?

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Ashi

• November 16, 2020 19:48

I am trying to run BaseRecalibrator with my WGS data of human cancer samples according to current GATK best practice.

My reference genome is hg19.

 

To run BaseRecalibrator, I need known SNP, Indel files.

I found these files in b37 version in gs://gatk-legacy-bundles, but no files for hg19.

Does anyone know where I can get these files?  

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  Genevieve Brandt (she/her)

  • November 17, 2020 21:35

  Ashi this has been previously discussed on the forum: https://gatk.broadinstitute.org/hc/en-us/community/posts/360074098891-Picard-liftover-error-Output-vcf-and-Reject-vcf-are-empty#community_comment_360013492612

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  Ashi

  • November 17, 2020 21:51

  Thanks for update! Will change reference from hg19 to hg38.

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