{"action":"created","issue":{"url":"https://api.github.com/repos/bulik/ldsc/issues/108","repository_url":"https://api.github.com/repos/bulik/ldsc","labels_url":"https://api.github.com/repos/bulik/ldsc/issues/108/labels{/name}","comments_url":"https://api.github.com/repos/bulik/ldsc/issues/108/comments","events_url":"https://api.github.com/repos/bulik/ldsc/issues/108/events","html_url":"https://github.com/bulik/ldsc/issues/108","id":303586374,"number":108,"title":"Validation of ldsc results","user":{"login":"yupenghe","id":11562802,"avatar_url":"https://avatars3.githubusercontent.com/u/11562802?v=4","gravatar_id":"","url":"https://api.github.com/users/yupenghe","html_url":"https://github.com/yupenghe","followers_url":"https://api.github.com/users/yupenghe/followers","following_url":"https://api.github.com/users/yupenghe/following{/other_user}","gists_url":"https://api.github.com/users/yupenghe/gists{/gist_id}","starred_url":"https://api.github.com/users/yupenghe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yupenghe/subscriptions","organizations_url":"https://api.github.com/users/yupenghe/orgs","repos_url":"https://api.github.com/users/yupenghe/repos","events_url":"https://api.github.com/users/yupenghe/events{/privacy}","received_events_url":"https://api.github.com/users/yupenghe/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-03-08T18:37:52Z","updated_at":"2018-03-08T22:46:58Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\nWith the help from documentation and previous issues, I have set up and run through ldsc pipeline for partitioned heritability analysis. However, I am not sure if I ran it in the correct way. Therefore, I am trying to validate the pipeline by reproducing the figure 6 in [Finucane et al](https://www.nature.com/articles/ng.3404), which shows the enrichment of trait-associated variants in different cell type groups. \r\n\r\nThe results I got are very different from ones in the figure and they are really confusing. For example, I found all cell type groups are associated with height but in the figure only three cell type groups are enriched. I may run the pipeline incorrectly but I could not figure it out. Could you please look it over? Thanks!\r\n\r\nBelow are what I did. First, I downloaded\r\n* summary statistics from https://data.broadinstitute.org/alkesgroup/sumstats_formatted/\r\n* baseline model from https://data.broadinstitute.org/alkesgroup/LDSCORE/1000G_Phase3_baselineLD_v1.1_ldscores.tgz\r\n* weights for baseline model from https://data.broadinstitute.org/alkesgroup/LDSCORE/weights_hm3_no_hla.tgz\r\n* cell type group information from https://data.broadinstitute.org/alkesgroup/LDSCORE/1000G_Phase3_cell_type_groups.tgz\r\n* SNP allele frequency data from https://data.broadinstitute.org/alkesgroup/LDSCORE/1000G_Phase3_frq.tgz\r\n\r\nThen, I ran the command (taking Height1 as an example) below to get the enrichment and p-value.\r\n```\r\npython2.7 ldsc.py --h2 \\\r\n       sumstats/PASS_Height1.sumstats.gz \\\r\n       --w-ld-chr weights_hm3_no_hla/weights. \\\r\n       --ref-ld-chr 1000G_Phase3_cell_type_groups/cell_type_group.1.,baselineLD_v1.1/baselineLD. \\\r\n       --frqfile-chr 1000G_Phase3_frq/1000G.EUR.QC. \\\r\n       --overlap-annot \\\r\n       --out ctg1_Height1 \\\r\n       --print-coefficients\r\n```"},"comment":{"url":"https://api.github.com/repos/bulik/ldsc/issues/comments/371651414","html_url":"https://github.com/bulik/ldsc/issues/108#issuecomment-371651414","issue_url":"https://api.github.com/repos/bulik/ldsc/issues/108","id":371651414,"user":{"login":"yupenghe","id":11562802,"avatar_url":"https://avatars3.githubusercontent.com/u/11562802?v=4","gravatar_id":"","url":"https://api.github.com/users/yupenghe","html_url":"https://github.com/yupenghe","followers_url":"https://api.github.com/users/yupenghe/followers","following_url":"https://api.github.com/users/yupenghe/following{/other_user}","gists_url":"https://api.github.com/users/yupenghe/gists{/gist_id}","starred_url":"https://api.github.com/users/yupenghe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yupenghe/subscriptions","organizations_url":"https://api.github.com/users/yupenghe/orgs","repos_url":"https://api.github.com/users/yupenghe/repos","events_url":"https://api.github.com/users/yupenghe/events{/privacy}","received_events_url":"https://api.github.com/users/yupenghe/received_events","type":"User","site_admin":false},"created_at":"2018-03-08T22:46:58Z","updated_at":"2018-03-08T22:46:58Z","author_association":"NONE","body":"I also tried the data based on 1000G phase 1 data and got very similar results, which are also different from what are present in the paper.\r\n\r\n* SNP allele frequency data from https://data.broadinstitute.org/alkesgroup/LDSCORE/1000G_Phase1_frq.tgz\r\n* baseline model from https://data.broadinstitute.org/alkesgroup/LDSCORE/1000G_Phase1_baseline_ldscores.tgz\r\n* cell type group data from https://data.broadinstitute.org/alkesgroup/LDSCORE/1000G_Phase1_cell_type_groups.tgz"}}
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