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Al-Murphy / MungeSumstats

Rapid standardisation and quality control of GWAS or QTL summary statistics
https://doi.org/doi:10.18129/B9.bioc.MungeSumstats
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different gwas column title to import #195

Closed songlyzz closed 1 week ago

songlyzz commented 1 week ago

Hi Murphy, I using some GWAS sumstats by plink 1.9 or 2, the summary titile contain : (1) SNP Allele1 Allele2 Freq1 FreqSE MinFreq MaxFreq Weight Zscore P Direction HetISq HetChiSq HetDf HetPVal CHR BP (2) "variant_id","chromosome","base_pair_location","effect_allele","other_allele","odds_ratio","p_value" (3) "SNP","CHR","BP","A1","A2","OR","P" (4) "ID","CHROM","POS","ALT","REF","or","PVAL" How can I deal with it, just rename them to "SNP","CHR","BP","A1","A2","OR","P" and use function format_sumstats(path = XX, ref_genome = "GRCh37", infer_eff_direction=TRUE ) ?

Al-Murphy commented 1 week ago

Hi! So Mungesumstats uses a mapping file so should be able to pick up and differing names of the column headers no matter the standard used. Please try running your sumstats as is but feel free to reopen if there are any errors with column headers. Also worth reading the related documentation as I believe this is covered there (if not, let me know as it should be!).

Cheers, Alan.