Include LD reference panel in bulk download

[jdblischak]

When I bulk downloaded the data*, I noticed that for the BST1 locus that there were 2 rows per SNP, and the only column that differed was MAF. This PR includes the column LD_ref to distinguish between the 2 rows.

Related questions:

1. How is the Freq column calculated? I was surprised that it is unchanged when using different LD panels. Is MAF calculated in the reference panel and Freq calculated in the study samples?

2. Is there a documentation page that describes each of the output columns in detail? I haven't been able to find it.

* Caveat: I didn't actually perform the bulk download from within the app. It always crashed at 87%. I extracted the code from app.R to combine all the results.

[jdblischak]

Is MAF calculated in the reference panel and Freq calculated in the study samples?

Update: that was just a guess. After looking at the data, it appears that Freq is always calculated from the UKB samples. It perfectly matches MAF when LD_ref == "UKB" but is off when LD_ref != "UKB". Is my interpretation correct?

[jdblischak]

@bschilder I'd appreciate any advice on my questions above

[bschilder]

Hi @jdblischak, apologies for the delay.

1. Freq/MAF: Freq and MAF come from the GWAS summary statistics when they're provided. If only Freq or MAF is provided, the other is inferred (e.g. 1-MAF=Freq). Of course, it's preferred that the user provide both, since this inference may be inaccurate in the case of multi-allelic SNPs. If neither col is available, echolocatoR tries to fill them in with the UKB reference panel.
2. Multiple rows/SNP: This occurs because some loci have been fine-mapped using multiple LD references panels (one row/LD ref). Did you programmatically check that they're actually all duplicated without any differences (besides MAF), or was this from a visual inspection? All the sum stats should be the same, but the fine-mapping results should be slightly different across LD panels.
3. Col descriptions: Making this a separate issue here Multi-finemap column descriptions #4.
4. Include LD ref in bulk download: I'll check this. Now here Include LD ref in bulk download #5.
5. Bulk download: Making this a separate issue here Bulk download failing #3 .