However, my sumstats are lifting, but without harmonizing:
INFO - Parsing input GWAS
INFO - loaded 7651549 variants
INFO - Performing liftover
INFO - 7651549 variants after liftover
INFO - Creating index to attach reference ids
INFO - Acquiring reference metadata
INFO - alligning alleles
INFO - 0 variants after restricting to reference variants
INFO - Ensuring variant uniqueness
INFO - 0 variants after ensuring uniqueness
INFO - Checking for missing frequency entries
INFO - Saving...
INFO - Finished converting GWAS in 142.95764788985252 seconds
And I get no error message.
My snp_reference meta-data looks like this:
chromosome position id allele_0 allele_1 allele_1_frequency rsid
1 1774334 chr1_1774334_A_G_b38 A G 0.948626151625909 chr1:1774334:SG
1 1774697 chr1_1774697_T_C_b38 T C 0.948619364368989 chr1:1774697:SG
And my sumstats:
id chr pos rs.id ref alt AF.alt mac num beta SE pval pval.noadj converged OR
339 chr1 693731 1:693731:A:G A G 0.106902117155606 2252 10533 -0.178771556135796 0.113841267586995 0.116331825589296 0.116331825589296 TRUE 0.836296924478001
349 chr1 705882 1:705882:G:A G A 0.0468052786480585 986 10533 -0.0471369452566297 0.167245157473858 0.778063584334615 0.778063584334615 TRUE 0.953956748792932
Hi, I am running gwas_parsing.py to harmonize and liftover gwas summary stats like this:
python3 summary-gwas-imputation/src/gwas_parsing.py \ -gwas_file all.saige.forMETAL_210617.txt.gz \ -output_column_map rs.id variant_id \ -output_column_map A2 non_effect_allele \ -output_column_map A1 effect_allele \ -output_column_map OR effect_size \ -output_column_map pval pvalue \ -output_column_map SE standard_error \ -output_column_map chr chromosome \ -output_column_map pos position \ -output_column_map num sample_size \ --chromosome_format \ -liftover hg19ToHg38.over.chain.gz \ -snp_reference_metadata saige_variants_b38_withoutchrX.txt.gz METADATA \ -output all.saige.b38.harm.txt \
However, my sumstats are lifting, but without harmonizing: INFO - Parsing input GWAS INFO - loaded 7651549 variants INFO - Performing liftover INFO - 7651549 variants after liftover INFO - Creating index to attach reference ids INFO - Acquiring reference metadata INFO - alligning alleles INFO - 0 variants after restricting to reference variants INFO - Ensuring variant uniqueness INFO - 0 variants after ensuring uniqueness INFO - Checking for missing frequency entries INFO - Saving... INFO - Finished converting GWAS in 142.95764788985252 seconds
And I get no error message.
My snp_reference meta-data looks like this: chromosome position id allele_0 allele_1 allele_1_frequency rsid 1 1774334 chr1_1774334_A_G_b38 A G 0.948626151625909 chr1:1774334:SG 1 1774697 chr1_1774697_T_C_b38 T C 0.948619364368989 chr1:1774697:SG
And my sumstats: id chr pos rs.id ref alt AF.alt mac num beta SE pval pval.noadj converged OR 339 chr1 693731 1:693731:A:G A G 0.106902117155606 2252 10533 -0.178771556135796 0.113841267586995 0.116331825589296 0.116331825589296 TRUE 0.836296924478001 349 chr1 705882 1:705882:G:A G A 0.0468052786480585 986 10533 -0.0471369452566297 0.167245157473858 0.778063584334615 0.778063584334615 TRUE 0.953956748792932
Thank you for your help. Best regards, Laura.