How to update the partitioned LDscore?

[Jesson-mark]

Hi,
thanks for the great software!

I'm using S-LDSC to partition herititability for my GWAS and our eQTLs datasets. I already created two types of annot files and LDscore files (containing two types of eQTLs: nominal eQTLs and max PIP of eQTLs) as that in GTEx.

I noticed that the LDscores of all annotations except eQTLs annotations are same in the two types of LDscore files. For example, the baseL2, Coding_UCSC.bedL2, ..., Human_Promoter_Villar_ExAC.flanking.500L2 are all same! Since calculating LDscore from the annot file is a little time-consuming (about 2.5 days for chr1), I wonder if I can calculate LDscore for the additional annotation then merge it with pre-calculated LDscore of other annotations?

[aksarkar]

Yes, you can append the new column name to the header and the new values to each row.

[Jesson-mark]

Thanks for your useful reply! I'll have a try.