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What's the difference between b37 and hg19 resources?

ihleeihlee Posts: 2Member

Hi, all. I have questions on resource bundles.
Are the 'hg19' bundle files just liftover from 'b37' bundles in UCSC-style? If so, why are there some variants in only one version and not the other? For example, the variant 'rs34872315 (on chr1)' is in b37 version of dbsnp137.excluding_sites_after_129.vcf, but not in hg19 version. At first, I thought it's because of the differences in reference genome (vcf files in the bundle are fit for the accompanying reference sequences). But the reference chromosome 1 was the same in both bundles. Can you help me to understand the difference between b37 and hg19 resource bundles?

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,530Administrator, GATK Developer admin

    Hi there,

    The two versions of the reference genomes are not exactly the same. There are a few differences, for example some bases that are flipped between strands. That is why we have liftover chain files to convert between the two versions. So there may be a few variants that are filtered out in one version relative to the other. But this should affect only a tiny proportion of variants.

    Geraldine Van der Auwera, PhD

  • ihleeihlee Posts: 2Member

    Yes, I expected a few differences in variant sets between one version and the other. But then, why were the accompanying reference sequence files the same? I diffed chromosome by chromosome between two fasta files, and only differences were chromosome M and Y.

  • trptyrphetrptyrphe huileixu@gmail.comPosts: 1Member

    Hi, I couldn't find the hg19Tob37 chain file in the bundle resources. Could you please let me know its updated location? Thanks.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,530Administrator, GATK Developer admin

    Everything we provide should be in the resource bundle; if it's not in there, we don't have it. Did you look in the bundle on our FTP, or just in the small resources directory in the downloaded package?

    Geraldine Van der Auwera, PhD

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