s-LDSC continuous annotations

[aiim-lab]

AIM: To produce continuous annotation files in UCSC bed format to perform partition LDSC using the continuous annotation files (I am following: [https://kevinlkx.github.io/analysis_pipelines/sldsc_pipeline.html#compute_ld_scores_for_continuous_annotations]

Hiccup: I have plink files (bim, bed, fam) for : 1000G.EUR.QC. which I hope could be used to produce continuous annotations and which eventually can be used in partition heritability analysis as : python ldsc.py \ --h2 ${TRAIT}.sumstats.gz \ --ref-ld-chr baselineLD.,${ANNOT}. \ --frqfile-chr 1000G_Phase3_frq/1000G.EUR.QC. \ --w-ld-chr 1000G_Phase3_weights_hm3_no_MHC/weights.hm3noMHC. \ --overlap-annot --print-cov --print-coefficients --print-delete-vals \ --out ${TRAIT}${ANNOT}_baselineLD where ${ANNOT} are the continuous annotations, I want to produce.

Thus, I want to figure out, how to produce these continuous annotations files which will eventually be used in partition heritability analysis and whose format should look like: ("chr", "start", "end", "value") as per the script: [https://github.com/kevinlkx/analysis_pipelines/blob/master/code/make_ldsc_continuous_annot.R]

[aksarkar]

Continuous annotations are typically the output of some other method/pipeline. In general, that other pipeline produces one value per SNP.

Without more information, it is not possible to help you produce continuous annotation files.

[aiim-lab]

I figured that continuous annotations are produced from some other pipeline. So, I grabbed them from pre-existing databases (cao et all) and using them in partition heritability analysis using LDSC. Closing the issue.