From 2fecc9f2bc8ca6d6ad2476e6847168e906e240e6 Mon Sep 17 00:00:00 2001
From: Gaddis <ngaddis@rti.org>
Date: Tue, 10 Mar 2020 11:44:46 -0400
Subject: [PATCH] [#3] Updated QC workflow README

---
 genotype_array_qc/README.md | 258 +++++++++++++++++++++++++++++++++++-
 1 file changed, 257 insertions(+), 1 deletion(-)

diff --git a/genotype_array_qc/README.md b/genotype_array_qc/README.md
index 5005752..69ea5ee 100644
--- a/genotype_array_qc/README.md
+++ b/genotype_array_qc/README.md
@@ -107,6 +107,26 @@ Parameters:
 <details>
 <summary>3. Remove duplicate IDs (based on call rate)</summary>
 
+Sample command:
+``` shell
+```
+
+Input Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Output Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Parameters:
+
+| PARAMETER | DESCRIPTION |
+| --- | --- |
 </details>
 
 
@@ -135,7 +155,6 @@ Input Files:
 
 | FILE | DESCRIPTION |
 | --- | --- |
-| `[PREFIX_LIST]` | List of prefixes of files to be merged |
 
 
 Output Files:
@@ -197,66 +216,303 @@ Parameters:
 <details>
 <summary>7. Format phenotype data to standard format</summary>
 
+Sample command:
+``` shell
+```
+
+Input Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Output Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Parameters:
+
+| PARAMETER | DESCRIPTION |
+| --- | --- |
 </details>
 
 
 <details>
 <summary>8. Structure workflow (separate supporting workflow)</summary>
 
+Sample command:
+``` shell
+```
+
+Input Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Output Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Parameters:
+
+| PARAMETER | DESCRIPTION |
+| --- | --- |
 </details>
 
 
 <details>
 <summary>9. Partition data by ancestry</summary>
 
+Sample command:
+``` shell
+plink \
+    --bfile [INPUT_BED_BIM_FAM_PREFIX] \ \
+    --keep [KEEP_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 |
+| `[KEEP_LIST]` | List of subjects to keep |
+
+
+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 |
+| `--keep [KEEP_LIST]` | List of subjects to keep |
+| `--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 |
 </details>
 
 
 <details>
 <summary>10. Call rate filter</summary>
 
+Sample command:
+``` shell
+```
+
+Input Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Output Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Parameters:
+
+| PARAMETER | DESCRIPTION |
+| --- | --- |
 </details>
 
 
 <details>
 <summary>11. HWE filter</summary>
 
+Sample command:
+``` shell
+```
+
+Input Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Output Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Parameters:
+
+| PARAMETER | DESCRIPTION |
+| --- | --- |
 </details>
 
 
 <details>
 <summary>12. Subject call rate filter (based on autosomes)</summary>
 
+Sample command:
+``` shell
+```
+
+Input Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Output Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Parameters:
+
+| PARAMETER | DESCRIPTION |
+| --- | --- |
 </details>
 
 
 <details>
 <summary>13. Relatedness workflow (separate supporting workflow)</summary>
 
+Sample command:
+``` shell
+```
+
+Input Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Output Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Parameters:
+
+| PARAMETER | DESCRIPTION |
+| --- | --- |
 </details>
 
 
 <details>
 <summary>14. Remove samples based on relatedness</summary>
 
+Sample command:
+``` shell
+```
+
+Input Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Output Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Parameters:
+
+| PARAMETER | DESCRIPTION |
+| --- | --- |
 </details>
 
 
 <details>
 <summary>15. Sex check and sample removal</summary>
 
+Sample command:
+``` shell
+```
+
+Input Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Output Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Parameters:
+
+| PARAMETER | DESCRIPTION |
+| --- | --- |
 </details>
 
 
 <details>
 <summary>16. Excessive homozygosity filtering</summary>
 
+Sample command:
+``` shell
+```
+
+Input Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Output Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Parameters:
+
+| PARAMETER | DESCRIPTION |
+| --- | --- |
 </details>
 
 
 <details>
 <summary>17. Set het haploids to missing</summary>
 
+Sample command:
+``` shell
+```
+
+Input Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Output Files:
+
+| FILE | DESCRIPTION |
+| --- | --- |
+
+
+Parameters:
+
+| PARAMETER | DESCRIPTION |
+| --- | --- |
 </details>