Plink GWAS on RAP produces a single txt output file
plink_gwas.plink2.PHENO1.glm.logistic.assoc.txt
The file has 12 columns
#CHROM POS ID REF ALT A1 TEST OBS_CT OR LOG(OR)_SE Z_STAT P
The file I got had 5.5 million rows.
The file had 200,000 duplicates. In order to use LocusZoom and get a correct Manhattan Plot and qqPlot the duplicates must be removed. How do I do that?
Comments
3 comments
Can you select those files and just remove them? Or maybe not upload them to the platform to begin with.
Plink GWAS on RAP produces a single txt output file
plink_gwas.plink2.PHENO1.glm.logistic.assoc.txt
The file has 12 columns
#CHROM POS ID REF ALT A1 TEST OBS_CT OR LOG(OR)_SE Z_STAT P
The file I got had 5.5 million rows.
The file had 200,000 duplicates. In order to use LocusZoom and get a correct Manhattan Plot and qqPlot the duplicates must be removed. How do I do that?
I see. You would need to write a script to remove duplicate. Then you can use swiss-army-knife to run that python script on your file.
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