Only 1 SNP left after filtering

[zlm2018]

Thank you very much for developing the method.

I encountered some problems when running the code. I used the GWAS summary data with the GWAS catalog code GCST007799 (trait adult onset asthma in your paper), and only 1 SNP left after filtering, which hindered the LDSC regression. The error is as the following:

File "/gsMap-main/src/gsMap/utils/jackknife.py", line 32, in _check_shape
raise ValueError("More dimensions than datapoints.")
ValueError: More dimensions than datapoints.

Could you please find out the reasons for the error? Thank you very much.

[LeonSong1995]

I was able to run gsMap successfully using this GWAS data. Could you please try the following code:

## Download GWAS summary
wget https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST007001-GCST008000/GCST007799/ADULT1_ADULT2_ONSET_ASTHMA.20180716.allchr.assoc.GC.gz

## Format the summary statistics
gsmap format_sumstats \
--sumstats ADULT1_ADULT2_ONSET_ASTHMA.20180716.allchr.assoc.GC.gz \
--out ADULT1_ADULT2_ONSET_ASTHMA.20180716.allchr.assoc.GC \
--snp SNP \
--a1 ALLELE1 \
--a2 ALLELE0 \
--info INFO \
--beta BETA \
--se SE \
--p P_GC \
--n N

Here is the log from my test run: