From 87964f195756bc9b04ea74156a858f4792f56acf Mon Sep 17 00:00:00 2001
From: Gaddis <ngaddis@rti.org>
Date: Thu, 12 Mar 2020 14:24:48 -0400
Subject: [PATCH] [#7] Added README.md for LD pruning workflow

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 genotype_array_qc/ld_pruning/README.md | 97 ++++++++++++++++++++++++++
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+# LD Pruning
+
+## Introduction
+
+This document details the standard analysis workflow for performing LD pruning of genotypes. An automated pipeline, developed using WDL, Cromwell, and Docker, is available for this workflow.
+
+This workflow takes the following inputs:
+1. Genotypes in PLINK bed/bim/fam format
+2. Values for window size, step size, and r^2 threshold for pruning (see https://www.cog-genomics.org/plink/1.9/ld)
+
+This workflow generates the following outputs:
+1. LD-pruned genotypes in bed/bim/fam format
+
+## Workflow
+
+The steps in this workflow are as follows:
+<details>
+<summary>1. Generate pruning lists</summary>
+
+Sample command:
+```
+plink \
+    --bfile [INPUT_BED_BIM_FAM_PREFIX] \
+    --indep-pairwise [WINDOW_SIZE] [STEP_SIZE] [RSQ_THRESHOLD] \
+    --out [OUT_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 |
+| --- | --- |
+| `[OUT_PREFIX].prune.in` | List of variants in approximate linkage equilibrium |
+| `[OUT_PREFIX].prune.out` | List of excluded variants |
+| `[OUT_PREFIX].log` | PLINK log file |
+
+
+Parameters:
+
+| PARAMETER | DESCRIPTION |
+| --- | --- |
+| `--bfile [INPUT_BED_BIM_FAM_PREFIX]` | Prefix for input genotypes in PLINK bed/bim/fam format |
+| `--window_size [WINDOW_SIZE]` | Window size to use for call to `--indep-pairwise` |
+| `--step_size [STEP_SIZE]` | Step size to use for call to `--indep-pairwise` |
+| `--rsq_threshold [RSQ_THRESHOLD]` | R-squared threshold to use for call to `--indep-pairwise` |
+| `--out [OUTPUT_PREFIX]` | Prefix for output files |
+</details>
+
+
+<details>
+<summary>2. Generate LD pruned genotype files</summary>
+
+Sample command:
+```
+plink \
+    --bfile [INPUT_BED_BIM_FAM_PREFIX] \
+    --extract [PRUNE_IN_FILE] \
+    --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 |
+| `[PRUNE_IN_FILE]` | List of variants in approximate linkage equilibrium from step 1 |
+
+
+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 |
+| `--prune_in [PRUNE_IN_FILE]` | List of variants in approximate linkage equilibrium from step 1 |
+| `--out [OUTPUT_BED_BIM_FAM_PREFIX]` | Prefix for output genotypes in PLINK bed/bim/fam format |
+</details>