What database to use for GATK baseRecalibration when using the ensembl hg19 genome
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10 days ago

I am running gatk base recalibrator as part of a pipeline (sarek), and it requires --dbsnpor--known_indels. I am using the regular ensembl hg38.fa.gz (https://hgdownload2.soe.ucsc.edu/goldenPath/hg38/bigZips/). The number of files in ensembl genome download is overwhelming (https://hgdownload2.soe.ucsc.edu/downloads.html) and I don't know what to use for dbsnp that would correspond to this. Do you have any suggestions? Where can I learn about all the various versions and annotation files for the human genomes?

ensembl gatk • 208 views
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10 days ago
GenoMax 143k

While you have referred to hg19 in title you seem to be using hg38 (latest genome build) in the rest of the text. So assuming that you are interested in hg38 you can find the GATK resource bundle useful where you should download all files (including genome/indexes and SNP files): https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0/

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