From e16c108c66213d0dd536f9eee1027d8f6c0b0dcd Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 12 Feb 2024 17:14:51 +0100 Subject: Change lmm mode to 9 --- gn/runner/gemma.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gn') diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm index 89b6482..131284a 100644 --- a/gn/runner/gemma.scm +++ b/gn/runner/gemma.scm @@ -55,7 +55,7 @@ (let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --parallel -- -gk -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt > " k-json-fn )))] (if (not (= err 0)) (exit err))) - (let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --name \"" name "\" --id \"" ids "\" --trait \"" trait-name "\" --verbose --loco --json --parallel --input " k-json-fn " -- -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt -lmm 2 -maf 0.1 > " gwa-json-fn)))] + (let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --keep --population \"" population "\" --name \"" name "\" --id \"" ids "\" --trait \"" trait-name "\" --verbose --loco --json --parallel --input " k-json-fn " -- -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt -lmm 9 -maf 0.1 > " gwa-json-fn)))] (if (not (= err 0)) (exit err))) (delete-file pheno-fn) -- cgit v1.2.3