Help with the input files

[bitcometz]

hello,

I am trying to run the script run_ldsc_reg.sh, but I do not the formats of the following files:

sumstats_taskfile=/n/groups/price/kushal/LDSC/ldsc/TASKFILES/sumstats_reduced_blood.txt
annot_taskfile=/n/groups/price/kushal/Enhancer_MasterReg/data/temp.txt

Could you provide an eample for the above files ?

Best

[kkdey]

Hi @bitcometz, threse are just files that contain the summary statistics

head -n 5 /n/groups/price/kushal/LDSC/ldsc/TASKFILES/sumstats_reduced_blood.txt
UKB_460K.blood_RBC_DISTRIB_WIDTH.sumstats
UKB_460K.blood_RED_COUNT.sumstats
UKB_460K.blood_WHITE_COUNT.sumstats
UKB_460K.blood_PLATELET_COUNT.sumstats
UKB_460K.blood_EOSINOPHIL_COUNT.sumstats

For the annot_taskfile, I just used it to pass names of annotation folderss, example from the Enhancer-driven paper: https://www.biorxiv.org/content/10.1101/2020.09.02.279059v3

head -n 3 $annot_taskfile

EDS_Binary_top10
eQTL_CTS_prob
Expecto_MVP

The annotation folder has the following strcuture

-Annotation folder (gene score specific)
   -  S2G1 folder (may be 100kb) 
   -  S2G2 folder (may be ABC)
   -

Hope this is clear

[bitcometz]

thanks !!!