From 0e39848f46042b1f7bac1641bb22f4a0736feb8b Mon Sep 17 00:00:00 2001 From: Gaddis Date: Tue, 10 Mar 2020 14:18:15 -0400 Subject: [PATCH] [#3] Updated QC workflow README --- genotype_array_qc/README.md | 19 ++++++++++++++++++- 1 file changed, 18 insertions(+), 1 deletion(-) diff --git a/genotype_array_qc/README.md b/genotype_array_qc/README.md index b245180..2902853 100644 --- a/genotype_array_qc/README.md +++ b/genotype_array_qc/README.md @@ -549,28 +549,45 @@ Parameters:
-15. Remove samples based on relatedness +15. Remove samples based on relatedness (optional) Sample command: ``` shell +plink \ + --bfile [INPUT_BED_BIM_FAM_PREFIX] \ + --remove [REMOVE_LIST] \ + --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 | +| `[REMOVE_LIST]` | List of subjects to remove | 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 | +| `--remove [REMOVE_LIST]` | List of subjects to remove | +| `--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 |