hs37d5 genome in the GATK bundle

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Rea Kalampaliki

• February 17, 2022 10:16
• Edited

Following a previous post: BaseRecalibrator - no suitable codecs – GATK (broadinstitute.org)

I think that my problem lies on not choosing correctly the reference genome for my samples. I was given the samples without the reference genome FASTA file. My samples come from the 1000 Genome Project Phase 3. With a bit of research I discovered that the reference genome for these samples were the hs375d reference genome.

Is this reference genome available in the GATK-bundle (FASTA and VCFs with known variants) ?

Thank you.

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  Genevieve Brandt (she/her)

  • February 17, 2022 21:18

  Hi Rea Kalampaliki,

  All of our resources available are outlined on our Resource Bundle page: https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle.

  I believe most of our resources are Grch38/hg38 and b37/hg19, unfortunately. I'm not familiar with hs375d so I'm not sure where you can find resources for that reference version.

  Best,

  Genevieve

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  Rea Kalampaliki

  • February 18, 2022 15:12

  Thank you,

  Homo_sapiens_assembly19_1000genomes_decoy_Homo_sapiens_assembly19_1000genomes_decoy.fasta seems to match to hs37d5.

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  Genevieve Brandt (she/her)

  • February 18, 2022 19:14

  Great! Glad you found what you were looking for.

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