Alan Murphy

Just to add to @jcotney solution, ENCODE also have a pipeline to produce this data (which could be replicated in nextflow I guess): https://github.com/ENCODE-DCC/chip-seq-pipeline2

Not sure if you are aware @combiz

@bschilder can you add the top 10 or so rows of the log file of the dropped non-biallelic SNPs from Example 1: ieu-a-8 or Example 2: Vuckovic2020?

I have checked MSS code and it seems to work as I suspect it to, it appears that there are now just a lot more alternative alleles in bioconductor's dbSNP...

I randomly picked 3 SNPs from my example code above and checked them in NCBI dbSNP online portal (dbSNP 155) and they all appear to be non-biallelic as described: [rs9824539](https://www.ncbi.nlm.nih.gov/snp/?term=rs9824539)...

Had a look into all the RS ID's from dbSNP 144 to check the proportion that are non-biallelic across the dbSNP 155 database and 144. I used an approach separate...

Posted on Biostars about this issue and got some replies too - https://www.biostars.org/p/9534249/#9534468 Generally, seems like people agree that the observed numbers are true

I think those 2 points highly depend on the downstream analysis use case. I do agree though, I feel dropping non-bi-allelic SNPs is no longer a sensible option given the...

Hey, >using MungeSumtats, with all up-to-date packages from Bioconductor 3.18 Yes, this is the latest release version of MSS. >Is the solution that this is simply due to higher coverage...

Hey @AhmedArslan, You are right that this will affect any function used by MSS that uses the dbSNP reference dataset (which is quite a lot - look for any function...