Entering edit mode
4.5 years ago
rsnewbie
•
0
I submitted some rs nums to Variant Effect Predictor, pushed returned ... no results!
What am I doing wrong?
There were about 40 empty data fields in the reported file.
I want to find the MAFs of a list of SNPs.
When I click on the preview run, the MAF is returned.
Yet, when I submit a batch, none of the MAFs are reported.
This should be super simple!
This is the file that I retrieve from VEP.
Almost all the fields are empty.
What is especially strange is that when I perform the instant run, it tells me the MAF is 0.1208, though
this information is not given when I push the run button.
Are you running online VEP against GRCh37 as well? If not, you'd see different results as co-ordinates don't match between v37 and v38.
Thank you RAMRS! When technology makes us frustrated, it is reassuring that others can help provide guidance.
GRCh37 does appear to give more info than GRCh38, though not the MAF.
I am unclear what I could be doing wrong. This should be a super simple error free request. Too bad the dbsnp batch request service is no longer available. It was such an easy online tool. Does no one offer such a tool now. Others comments that I have read on biostars and elsewhere have noted that rs MAF tools are not easy to find online now.
No, it does not. VEP supports GRCh38 more than GRCh37. Your VEP cache version is 37. MAF is an ambiguous term - where are you looking to get this information from - 1000 genomes/ExAC/gnomAD? From your value of 0.1208, you're looking for the 1000g global MAF.
Note that the position of rs7414 is 22:18075053 in GRCh37, while it is 22:17592287 in GRCh38. If your VEP cache has gnomAD files, I don't see why the annotated VCF does not have gnoomAD frequencies. Can you share the exact VEP command you used please?
Yes, the comment about GRCh37 having more info than GRCh38 did not make sense to me either. I probably changed the input fields.
I retried VEP and now MAF are appearing. Yeah! The output is below. I am very unclear what caused the change.
Here is the command line. I am still not receiving an MAF for gnomeAD.
Hmm, perhaps it is because I went away from the site and refreshed that I am now obtaining the MAFs.
Great!
I was having trouble with the file formats available with VEP. The pipes were not forming proper columns.
When I simply copy and paste my list of rsnums, formatting is perfect.
I have found that the easiest input format for VEP is tabular pseudo-VCF:
You can separate each column with a space or a tab, I've formatted the example below so it looks good:
There is a variety of file formats you can use with the Ensembl VEP: https://www.ensembl.org/info/docs/tools/vep/vep_formats.html#input
That is true. I just prefer the pseudo-VCF format because of the custom ID column that makes it easier to map input back to output.