hakyim
commented
4 days ago Forwarding to the mailing list.
Can you tell what is the overlap between your snps and UKB?
Festus: any ideas what could be wrong here?
Thanks Haky
---------- Forwarded message --------- From: Davidseye @.> Date: Mon, Jul 1, 2024 at 7:41 AM Subject: [hakyimlab/MetaXcan] after gwas_parsing.py(liftover) ,only 10% snp left (Issue #197) To: hakyimlab/MetaXcan @.> Cc: Subscribed @.***>
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_R10_K11_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 : image.png (view on web) https://github.com/hakyimlab/MetaXcan/assets/92795943/55767b15-f189-414b-9b8b-0a41274b8d16
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.
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Davidseye
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_R10_K11_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.