Converting txt.gz to PLINK bim
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11 weeks ago
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Hello, I'm trying to do a stratified LDSC (or S-LDSC/partitioned LDSC) between locus of interest and diseases (diabetes, arthritis, etc.). For locus of interest, I have a bed file from previous research. For diseases, I have downloaded GWAS sumstats from the GWAS atlas.

I have been using this documentation:

https://github.com/bulik/ldsc/wiki/LD-Score-Estimation-Tutorial#partitioned-ld-scores.

Though I have the bed file for locus of interest, GWAS sumstats come in a txt.gz format. However, the documentation says I need a PLINK bim file. Is there a way to get over this hurdle - say, convert the txt.gz file to a PLINK bim file? Thank you for your help in advance.

S-LDSC file LDSC format • 221 views
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