Where to find known sites for mm39 used by GATK4 BaseRecalibrator?

Question

[乙]

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.

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

Thank you in advance.

[乙]

bumping this question...

Answer 1

[乙]

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

There are various ways to access the FTP directory.