Hi, I've been struggling with the coordination step. I get a very low number of SNPs retained after filtering, even though the filters themselves list a number of SNPs that don't add up. Please see below
`
ldpred coord --rs SNP --A1 Effect_allele --A2 Non_effect_allele --pos POS --chr CHR --pval pval --eff Effect --ssf-format CUSTOM --eff_type LINREG --N 159095 --se se --max-freq-discrep 0.5 --vgf tmp-dir/DATA1 --ssf tmp-dir/SUMMSTATS.txt.gz --reffreq EFFECT_AF --out RES.coord --gf tmp-dir/LD_panel
------------------------------ Summary statistics ------------------------------
Num SNPs parsed from sum stats file 444335
Num invalid P-values in sum stats 1881
--------------------------------- Coordination ---------------------------------
Num individuals in LD Reference data: 504
SNPs in LD Reference data: 2697305
SNPs in Validation data: 602645
Num chromosomes used: 22
SNPs common across datasets: 441344
SNPs retained after filtering: 782
SNPs w ambiguous nucleotides filtered: 2625
SNPs w other nucleotide discrepancies filtered: 105
SNPs w MAF<0.010 filtered: 28
-------------------------------- Running times ---------------------------------
Run time for parsing summary stats: 5 min and 58.96 sec
Run time for coordinating datasets: 16 min and 51.44 sec
================================================================================`
Hi, I've been struggling with the coordination step. I get a very low number of SNPs retained after filtering, even though the filters themselves list a number of SNPs that don't add up. Please see below
`
ldpred coord --rs SNP --A1 Effect_allele --A2 Non_effect_allele --pos POS --chr CHR --pval pval --eff Effect --ssf-format CUSTOM --eff_type LINREG --N 159095 --se se --max-freq-discrep 0.5 --vgf tmp-dir/DATA1 --ssf tmp-dir/SUMMSTATS.txt.gz --reffreq EFFECT_AF --out RES.coord --gf tmp-dir/LD_panel
------------------------------ Summary statistics ------------------------------
Num SNPs parsed from sum stats file 444335
Num invalid P-values in sum stats 1881
--------------------------------- Coordination ---------------------------------
Num individuals in LD Reference data: 504
SNPs in LD Reference data: 2697305
SNPs in Validation data: 602645
Num chromosomes used: 22
SNPs common across datasets: 441344
SNPs retained after filtering: 782
SNPs w ambiguous nucleotides filtered: 2625
SNPs w other nucleotide discrepancies filtered: 105
SNPs w MAF<0.010 filtered: 28
-------------------------------- Running times ---------------------------------
Run time for parsing summary stats: 5 min and 58.96 sec
Run time for coordinating datasets: 16 min and 51.44 sec
================================================================================`