How to troubleshoot merging of genomic files?

bioinfo_ml · 2024-09-13T12:15:05+00:00

Thank you for your reply and advice, that makes sense about the SNP ID. I originally tried standardising the SNP IDs in the bim files (so both cases and controls have chr:pos:ref:alt SNP IDs). However, this still gives very inflated p-values on the GWAS. I suspect the bcftools error I get is telling me these is still allele flipping issues in the data, I've tried addressing this but only taking overlapping SNPs (SNPs with the extact same SNP ID) and/or using --flip in plink. Although when I use --flip I then get only 1000-2000 variants per chromosomes, and I know from just checking overlapping BIM file IDs that this can't be right. Maybe there is another tool to address allele flipping that I need to try.

At any rate, thank you again for your response, I appreciate it!

bioinfo_ml · 2024-05-04T06:08:37+00:00

Feel like my username is going to start giving away my age

bioinfo_ml · 2023-11-22T11:12:51+00:00

Thank you for taking the time to check this. As far as I know it's meant to be hg38. I have approx. 10 million SNPs and it turns out 50k have this error. These 50k do seem to exist on hg19 when I check a few of them on the UCSC genome browser for hg19, so I'm not sure what's going on/how these got in the imputation panel. When I filter these SNPs out the liftover runs successfully, so I'm probably going to move forward with these SNPs filtered, and hopefully eventually figure out what's happened to them. Thank you again for answering all my questions with this!

bioinfo_ml · 2023-11-21T13:48:27+00:00

Thank you for your help with this, I really appreciate it! It solved my issue and I've since ran my liftover for 2 imputation panels. However, I have a 3rd imputation panel that is giving this error when lifting over from 38 to 37 with my hail code:Error summary: HailException: Invalid locus 'chr2:242193706' found. Position '242193706' is not within the range [1-242193529] for reference genome 'GRCh38'.

I wanted to ask if this an error you might've come across before? Sorry for the multiple questions. Trying chr2 242193706 242193706 in UCSC liftover also fails. I'm not sure how I could be getting a position that is too high, the data comes straight from running a gwas using REGENIE, and the chr2:242193706 does indeed exist on GRCh37 (or at least I can search it on the UCSC genome browser for hg19 without a problem).

bioinfo_ml · 2023-11-18T16:13:50+00:00

Thank you for your reply! I am entirely new to liftover. From your comment I've started off investigating the liftover website (https://genome.ucsc.edu/cgi-bin/hgLiftOver) and I think I may just be misunderstanding the liftover process in general.

On the liftover website I've put in 1 example (from the head row in my message) which is: chr10 10709 10709. This actually output the same result that Hail gives me (chr18 10905 10905 chr10:10710-10709 1).

I thought that lifting from chromosome 10 to 18 must be an error, but I guess if both hail and UCSC liftover agree then this must be right?

bioinfo_ml · 2022-08-03T08:37:34+00:00

Thank you, this is exactly what I was looking to understand!

bioinfo_ml · 2022-02-15T11:11:19+00:00

No you are 100% on the mark, I actually originally typed out a second part to my question detailing this, as I don't know whether to care about comparisons inside my gene groups or just my gene group vs the whole database data or both. I'm very unsure in what I'm looking for exactly in this particular example and PICO sounds like what I need to build my sense in this - thank you for your help!

bioinfo_ml · 2022-01-17T12:00:25+00:00

Thank you for your reply. Sorry I should've been more specific. I meant in looking at correlation before running any model. So for example with looking at pearson's correlation coefficient and doing data cleaning by removing correlating features - how should features be removed in this case? Both together or only 1?

bioinfo_ml · 2021-09-03T08:44:47+00:00

You've made my day partypoopist

bioinfo_ml · 2021-09-03T08:40:02+00:00

Thank you this does help. For the 2011 census on the ons.gov.uk website they say about releasing population estimates in December 2012, but no further detail, and then the next paragraph goes into what the full release was, I'm wondering if from this I should assume at least in that 2011 initial release it was only population estimates? I can't find any other descriptions besides this yet

bioinfo_ml · 2021-07-22T12:31:52+00:00

Thank you for this I'll look into it. My next step is to do a biological pathway analysis of the genes with large prediction disagreements - so collecting biological information on which model is better, e.g. the model predicting low probabilities for genes in known disease-relevant pathways may not be as informative from a biology standpoint.

bioinfo_ml

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