Getting the db SNP VCF file for GRCh38.p13
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16 months ago
nhaus ▴ 100

Hello everybody,

after searching a long time, I am still unable to find the db SNP VCF file with the coordinatse for GRCh38.p13. The latest version of the db SNP VCF that I found was this here.

However, after downloading it, I realized, that it uses GRCh38.p12.

For context, I need the VCF file for the GATK BaseRecalibrator command.

I already aligned all my reads to the GRCh38.p13 reference which took quite some time, so I'd prefer if I dont have to realign everything to GRCh38.p12.

I am very new to the whole field, so my guess is that using the "GRCH38.p12 version" of the db SNP VCF file is not possible if i want to use the BaseRecalibrator for my BAM file which was generated with GRCh38.p13.

Any help is appreciated!

Thank you very much!

SNP dbSNP VCF • 977 views
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Entering edit mode
16 months ago

You can find it on GATK bundle : ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/

more information : https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle

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I have downloaded the latest version from that site, but that is VCF uses GRCh38.p2 instead of GRCh38.p13, which I require.

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