after gwas_parsing.py(liftover) ,only 10% snp left

[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.

[hakyim]

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. — Reply to this email directly, view it on GitHub <#197>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAW2ROKNDGHUNYXIK5Q3FY3ZKFFBPAVCNFSM6AAAAABKFP7YFSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGM4DGNZUHA2TSOA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Davidseye]

it works successfully in UKB' gwas file , and it also passed spredixcan step, 85% snp in the model.