From 9c060d66b0edc664a825e02a258d2406fd505517 Mon Sep 17 00:00:00 2001 From: Gaddis Date: Tue, 10 Mar 2020 13:06:20 -0400 Subject: [PATCH] [#3] Updated QC workflow README --- genotype_array_qc/README.md | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/genotype_array_qc/README.md b/genotype_array_qc/README.md index 69ea5ee..4848b7c 100644 --- a/genotype_array_qc/README.md +++ b/genotype_array_qc/README.md @@ -313,24 +313,40 @@ Parameters: Sample command: ``` shell +plink \ + --bfile [INPUT_BED_BIM_FAM_PREFIX] \ \ + --geno [CALL_RATE_THRESHOLD] \ + --make-bed \ + --out [OUTPUT_BED_BIM_FAM_PREFIX] ``` Input Files: | FILE | DESCRIPTION | | --- | --- | +| `[INPUT_BED_BIM_FAM_PREFIX].bed` | PLINK format bed file for input genotypes | +| `[INPUT_BED_BIM_FAM_PREFIX].bim` | PLINK format bim file for input genotypes | +| `[INPUT_BED_BIM_FAM_PREFIX].fam` | PLINK format fam file for input genotypes | Output Files: | FILE | DESCRIPTION | | --- | --- | +| `[OUTPUT_BED_BIM_FAM_PREFIX].bed` | PLINK format bed file for output genotypes | +| `[OUTPUT_BED_BIM_FAM_PREFIX].bim` | PLINK format bim file for output genotypes | +| `[OUTPUT_BED_BIM_FAM_PREFIX].fam` | PLINK format fam file for output genotypes | +| `[OUTPUT_BED_BIM_FAM_PREFIX].log` | PLINK log file | Parameters: | PARAMETER | DESCRIPTION | | --- | --- | +| `--bfile [INPUT_BED_BIM_FAM_PREFIX]` | Prefix for input genotypes in PLINK bed/bim/fam format | +| `--geno [CALL_RATE_THRESHOLD]` | Call rate threshold for excluding SNPs (e.g., 0.01) | +| `--make-bed` | Flag indicating to generate genotypes in PLINK bed/bim/fam format | +| `--out [OUTPUT_BED_BIM_FAM_PREFIX]` | Prefix for output genotypes in PLINK bed/bim/fam format |