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LD Score Regression (LDSC)
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Which --signed-sumstats? And NA genetic correlation #320

Open jielab opened 3 years ago

jielab commented 3 years ago

Hi, guys:

I am still confused with 2 basic things when running LDSC.

  1. If my GWAS have BETA, SE, Z, OR, how should I specify --signed-sumstats? Should it be "BETA,0" or "Z,0" or "OR,1"? Will this affect my output *.sumstats.gz file and downstream LDSC analysis? I know some software such as GCTA requires "Z" but NOT "BETA".

  2. For the example below, why eur_w_ld_chr is specified twice? If I change the second one to "--w-ld-chr weights_hm3_no_hla/", I get IndexError: list index out of range. What is happening here? 11

  3. For the analysis below, why the heritability of phentoype 1 is negative, and the genetic correlation is NA NA NA.

image

Your clarification is appreciated!

Best regards, Jie

Soulnature commented 2 years ago

I have got the same question, have you solved the question yet? if done, could you give me some advice， thank you！

jielab commented 1 year ago

The following code works fine now:

conda activate ldsc dir=/mnt/d/data/gwas/penguin ldscdir=/mnt/d/data/ldsc dat=A dats="B C D E F G" datf=$dir/$dat.gz head_row=zcat $datf | head -1 | sed 's/\t/ /g'; munge_sumstats.py --chunksize 10000 --sumstats $dat.tmp.gz \ --merge-alleles $ldscdir/w_hm3.snplist --out $dat \ --snp SNP --a1 EA --a2 NEA --ignore SNPID,OR \ --signed-sumstats BETA,0 --p P --N 100000

echo $dat $dats | sed -e 's/ /.sumstats.gz,/g' -e 's/$/.sumstats.gz/' | \ xargs -n1 -I % ldsc.py --rg % --out $dat.rg \ --ref-ld-chr $ldscdir --w-ld-chr $ldscdir

Jie