INQUISIT on a smaller list of SNPs

[marromesc]

Hi,

Loads of work on the package, congratulations!

I wonder if it can be run on a smaller set of SNPs. We performed fine mapping in the past ending up with a list of 26 SNPs and would like to know which of them are more relevant to regulating the neighbouring genes. Can we use INQUISIT for that with such a smaller set?

If yes, how does the input need to look like? I managed to run INQUISIT with your example BCACFM.CCVs.bed but didn't understand where columns 4-9 were coming from. Could you clarify this?

I really appreciate any help you can provide.

Kind regards, Maria

[jmbeesley]

Hi Maria

Yes you should be able to run of a small list of SNPs. Note that some of the datasets (e.g. the eQTL data) are targeted to specific breast cancer risk loci defined in Fachal, Nature Genetics 2020, so SNPs outside these regions will not include links to genes found using those methods.

The example file contains several columns that aren't really necessary for the analysis, but were retained in the file to link the variants back to the results from fine-mapping. So columns 4,5 and 6 are different IDs for the SNP (you could simply replicate column 4 three times); column 7 and 8 indicate the fine-mapped region and independent fine-mapped signal (you could use the index SNP in both columns); and column 9 was a phenotype association (any string would do).

Let me know if you need further info,

Jonathan

[marromesc]

Many thanks for your response, it worked smoothly! However, my list of SNPs didn't overlap coding or promoter regions so I needed to edit the scripts to stop running scripts dedicated to those regions to avoid error messages. You may consider checking SNPs' location and running only R scripts for regions overlapped by the SNPs in the input list.

Maria