Help in replicating heritability estimates

[littlehegemon]

I am trying to replicate the heritability estimates based on the insomnia GWAS summary statistics using LDSC. However, I have encountered a problem as my estimates seem to be only about half of the original estimates listed in Table S1. Despite my efforts to locate the error, I have been unsuccessful in finding the source of the problem.

Sex	h2 (Table S1)	h2_SE (Table S1)	h2 (my calculation)	h2_SE (my calculation)
Both (UKB)	0.0823	0.0036	0.0458	0.0021
Male (UKB)	0.0887	0.007	0.0438	0.0035
Female (UKB)	0.0906	0.0051	0.0542	0.0032

Below are the commands I used for female estimates.

zcat insomnia_female_ukb2b_EUR_sumstats_20190311_with_chrX_mac_100.txt.gz |cut -f 6,11,12,15,16,17 -d $'\t'|sed  "1s/STAT/Z/" > female_useful.txt
../munge_sumstats.py --sumstats  female_useful.txt --N-col NMISS --snp RSID_UKB   --a1 A1_UKB  --a2 A2_UKB --out female_insomnia_GWAS_2022 --merge-alleles LDSCORE_w_hm3.snplist --chunksize 500000
../ldsc.py --h2 female_insomnia_GWAS_2022.sumstats.gz --ref-ld-chr eur_w_ld_chr/ --w-ld-chr eur_w_ld_chr/ --out merged_GWAS_results_h2

The GWAS summary statistics for the female heritability were downloaded from

https://ctg.cncr.nl/documents/p1651/insomnia_female_ukb2b_EUR_sumstats_20190311_with_chrX_mac_100.txt.gz

I have tried to contact the first and corresponding authors but they seems to be too busy to reply. Can anyone tell me where am I wrong? Thanks.

[littlehegemon]

I have not taken prevalence into account. That's the problem.