The munging of 2 summary statistics started at 2025-03-04 23:19:55.113616
Reading in reference file
Reading summary statistics for GIANT_UKB_BMI_EUR_chr1.txt Yengo_Height_EUR_chr1.txt. Please note that this step usually takes a few minutes due to the size of summary statistic files.
All files loaded into R!



Munging file: GIANT_UKB_BMI_EUR_chr1.txt
Interpreting the SNP column as the SNP column.
Interpreting the A1 column as the A1 column.
Interpreting the A2 column as the A2 column.
Interpreting the BETA column as the effect column.
Interpreting the P column as the P column.
Interpreting the N column as the N column.
Interpreting the MAF column as the MAF column.
Interpreting the SE column as the SE column.
Merging file:GIANT_UKB_BMI_EUR_chr1.txt with the reference file:eur_w_ld_chr/w_hm3.snplist
175116 rows present in the full GIANT_UKB_BMI_EUR_chr1.txt summary statistics file.
94386 rows were removed from the GIANT_UKB_BMI_EUR_chr1.txt summary statistics file as the rs-ids for these rows were not present in the reference file.
No INFO column, cannot filter on INFO, which may influence results
4 rows were removed from the GIANT_UKB_BMI_EUR_chr1.txt summary statistics file due to missing MAF information or MAFs below the designated threshold of0.01
80726SNPs are left in the summary statistics file GIANT_UKB_BMI_EUR_chr1.txt after QC.
I am done munging file: GIANT_UKB_BMI_EUR_chr1.txt
The file is saved as BMI.sumstats.gz in the current working directory.



Munging file: Yengo_Height_EUR_chr1.txt
Interpreting the RSID column as the SNP column.
Interpreting the EFFECT_ALLELE column as the A1 column.
Interpreting the OTHER_ALLELE column as the A2 column.
Interpreting the BETA column as the effect column.
Interpreting the P column as the P column.
Interpreting the N column as the N column.
Interpreting the MAF column as the MAF column.
Interpreting the SE column as the SE column.
Merging file:Yengo_Height_EUR_chr1.txt with the reference file:eur_w_ld_chr/w_hm3.snplist
96851 rows present in the full Yengo_Height_EUR_chr1.txt summary statistics file.
7910 rows were removed from the Yengo_Height_EUR_chr1.txt summary statistics file as the rs-ids for these rows were not present in the reference file.
No INFO column, cannot filter on INFO, which may influence results
0 rows were removed from the Yengo_Height_EUR_chr1.txt summary statistics file due to missing MAF information or MAFs below the designated threshold of0.01
88941SNPs are left in the summary statistics file Yengo_Height_EUR_chr1.txt after QC.
I am done munging file: Yengo_Height_EUR_chr1.txt
The file is saved as Height.sumstats.gz in the current working directory.
     
Munging was completed at 2025-03-04 23:20:01.533907
The munging of all files took 0 minutes and 6.42029166221619 seconds
Please check the .log file(s) to ensure that all columns were interpreted correctly and no warnings were issued for any of the summary statistics files