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.
2 answers
The issue is resolved. I contacted the Sanger Institute and this was their reply:
There are various ways to access the FTP directory.
here is usable link https://ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-1505-SNPs_Indels/
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