samreenzafer

@nadineparker Any luck here? My runs give me similar Warnings for sigma ``` 2023/11/02/02:55:58 PM Checking for positive definiteness .. 2023/11/02/02:56:04 PM Checking for positive definiteness .. 2023/11/02/02:56:04 PM matrix...

Hi [AudeIkuzwe] Did you ever figure this out ? My input GWAS are all on African populations, so I was wondering if I should use a different reference panel as...

I created my own LDscores for Afr ethnicity, by extracting reported Africans from the 1000G cohort, excluding a few related samples (detected by KING), and extracting the HapMap3 snps (using...

Thanks for replying, none are provided by the Price lab, so I created my own , please see my previous comment to @AudeIkuzwe I'm not sure If my method and...

Hi Xihao, I have only these 13 variants in the `known_loci` . They are rare variants, and I don't want to prune them, since I specifically want to identify if...

I did try to run the `STAARpipelineSummary_Known_Loci_Pruning.r` script, but it gave me a NULL LDpruned file at the end. Maybe this is what is leading the `STAARpipelineSummary_Gene_Centric_Noncoding.r` script also to...

Thanks for the detailed response. 1) I do see that after pruning, by adjusting the maf_cutoff parameters, I get only 1 selected variant. Relaxing these parameters still give me the...

Same issue here, and then consequently the bedpeToBed12 is not working because of this. Did you figure this out?