Where to find known sites for mm39 used by GATK4 BaseRecalibrator?
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2.3 years ago
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Hi,

I always worked with the human genome performing different types of analysis with GATK. This time, I need to analyze the mouse genome (mus musculus) using the same pipeline as the one for humans. However, at the step of GATK BaseRecalibrator, I need to have the knownSites input files for the mouse (the equivalent to 1000G_omni2.5.hg38.vcf, Mills_and_1000G_gold_standard.indels.hg38.vcf and the dbSNP files in human).

The Sanger Mouse FTP seems to be down. I can't access their data.

enter image description here

Are these data available anywhere else? Otherwise, would a kind soul upload these data somewhere on the web?

Thank you in advance.

BaseRecalibrator mouse gatk • 1.1k views
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2.3 years ago
▴ 220

The issue is resolved. I contacted the Sanger Institute and this was their reply:

enter image description here

There are various ways to access the FTP directory.

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