Open Davidseye opened 2 months ago
when use code to liftover to hg38, here is my code: python /public/home/qihangm/sp.twas/summary-gwas-imputation-master/src/gwas_parsing.py \
-gwas_file /public/home/qihangm/sp.twas/gwas/cp/finngen_cp.all \ -liftover /public/home/qihangm/sp.twas/liftover/hg19ToHg38.over.chain.gz \ -output_column_map rsids variant_id \ -output_column_map ref non_effect_allele \ -output_column_map alt effect_allele \ -output_column_map beta effect_size \ -output_column_map pval pvalue \ -output_column_map sebeta standard_error \ -output_column_map pos position \ -output_column_map chrom chromosome \ --chromosome_format \ -output_column_map af_alt frequence \ --insert_value sample_size 196881 \ -snp_reference_metadata /public/home/qihangm/sp.twas/variant_metadata.txt.gz METADATA \ -output_order variant_id panel_variant_id chromosome position effect_allele non_effect_allele frequency pvalue zscore effect_size standard_error sample_size \ -output_column_map af_alt frequence \ -output /public/home/qihangm/sp.twas/gwas/cp/cp.txt
I only get : only 10% snp left . interestingly, when i use the same code to another gwas file (from UKB) ,it works well is the problem about my data' source? it's from finngen R10 gwas.
when use code to liftover to hg38, here is my code: python /public/home/qihangm/sp.twas/summary-gwas-imputation-master/src/gwas_parsing.py \
I only get :
only 10% snp left .
interestingly, when i use the same code to another gwas file (from UKB) ,it works well
is the problem about my data' source? it's from finngen R10 gwas.