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Reference VCF with "chr" contigs instead of "number"

Hello,

Can somebody point me out to a Hg38 vcf file that has the chromosome contigs labeled as "chr", and not with a number?

I am unable to find such file in the common repositories. The 1000 genome project does have some but they are rejected by GATK4 due to formatting issues.

Thanks Genaro

vcf reference-genome
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updated by Ram Ram • written by GPR GPR

1 answer

I am unable to find such file in the common repositories.

see under https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0/

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written by Pierre Lindenbaum Pierre Lindenbaum

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