“We provide a simple script (misc/estimate_lambdagc.py) to infer the genomic control factor to reinflate the summary statistics if it is unknown. The following script should be executed after step 1 completes.” I wonder if this estimate of GC lambda is the same as the GC lambda from ldsc.py?
For example:
Call:
./ldsc.py
--no-check-alleles
--h2 ./Trait5.sumstats.gz
--ref-ld-chr ./eur_w_ld_chr/
--out ./Trait5_h2
--w-ld-chr ./eur_w_ld_chr/
Total Observed scale h2: 0.002 (0.0013)
Lambda GC: 1.0046
Mean Chi^2: 1.0109
Intercept: 0.9948 (0.0071)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Mar 4 15:11:53 2024
Total time elapsed: 30.09s
I'm asking this because the GC lambda estimate from estimate_lambdagc.py is different from the GC lambda from ldsc
“We provide a simple script (misc/estimate_lambdagc.py) to infer the genomic control factor to reinflate the summary statistics if it is unknown. The following script should be executed after step 1 completes.” I wonder if this estimate of GC lambda is the same as the GC lambda from ldsc.py?
For example:
Call:
./ldsc.py
--no-check-alleles
--h2 ./Trait5.sumstats.gz
--ref-ld-chr ./eur_w_ld_chr/
--out ./Trait5_h2
--w-ld-chr ./eur_w_ld_chr/
Total Observed scale h2: 0.002 (0.0013)
Lambda GC: 1.0046
Mean Chi^2: 1.0109
Intercept: 0.9948 (0.0071)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Mar 4 15:11:53 2024
Total time elapsed: 30.09s
I'm asking this because the GC lambda estimate from estimate_lambdagc.py is different from the GC lambda from ldsc