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xqwen / fastenloc

Colocalization analysis of genetic association signals
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Format of fine-mapping results from SuSiE #27

Open Cosmos0112 opened 3 weeks ago

Cosmos0112 commented 3 weeks ago

Hi,

I'm trying to used fine-mapped results of complex traits from SuSiE as the input of fastENLOC as you recommended. I notice the following code you provided in input.md to help contrust the input file: summarize_dap2enloc.pl -dir dap_rst_dir -vcf snp_vcf_file [-tissue tissue_name] | gzip - > fastenloc.eqtl.annotation.vcf.gz

I wonder does each locus_id.postfix file in dap_rst_dir represent a causal signal derived from SuSiE? What information should each locus_id.postfix file include and what is the required format of this file? Additionally, what is the required format of snp_vcf_file? It would be better if you could provide some examples for these files.

Thanks!

xqwen commented 3 weeks ago

We are in the process of updating the repo for the release 3.1.

For converting SuSiE results, you should use susie2enloc in the utility directory. The syntax is unchanged.

The expected output format for SuSiE is now updated here

The SNP VCF file should list 

chromosome position snp_id ref_allele alt_allele

but without the INFO field.

We will upload examples soon.

Thanks!

xqwen commented 1 week ago

An example dataset and illustration have been added to the repo.

Let me know if you have further questions,

William