vcf file for mm10 dbsnp?

[JPreston]

Hello,

I have been trying to make a vcf file for mm10 dbsnp to use for GATK base quality recalibration and have been unsuccessful. Does anybody know where to download this file or what is the easiest way to make it?
I've tried downloading snp137.txt from ucsc and converting to vcf with GATK VariantsToVCF but that didn't work, it ran and produced an empty file.
Has anybody done this successfully?

Thanks in advance!

[dpryan]

It should be noted that the SNP database for mice is mostly differences between strains, which may or may not be appropriate for your uses. In general, one can just bootstrap this process and just avoid needing a background list of SNPs. This takes a bit of time, but it's the standard approach. This involves calling SNPs without the background VCF database, taking just the highest quality SNPs, rerunning with those SNPs as the background and then repeating until you get convergence.

[JPreston]

Thanks for the clarification! It makes sense that dbsnp would be incomplete for base quality recalibration with GATK. However, I have another (main) purpose for the vcf file, which is to filter snps sequenced in mouse tumors to remove false positives. Do you know of a way to make a vcf file for this purpose for mouse data? Thanks a lot!

[dpryan]

The normal method is bootstrapping, as mentioned above. I would strongly advise against it, but one could also just download other experiments with the same strain and call variants with that to use as a background. I don't recommend it because half of the time that strain is listed in a public dataset it ends up being incorrect and that some of the suppliers rejuvenate their stocks overtime, meaning that the background SNP distribution in your cohort may bear no resemblance to others published.

[id0]

I would also suggest looking into Mouse Genomes Project SNPs (they call SNPs separately for 17 different strains):

https://www.sanger.ac.uk/resources/mouse/genomes/

FTP:
ftp://ftp-mouse.sanger.ac.uk/