03-qc_plink.Rmd

---
params:
  project_name: !r gsub("(.*)_.*", "\\1", list.files(here::here(), pattern = ".Rproj$"))
  title: !r paste0("[", params[["project_name"]], "] Omni2.5 Array Quality-Control")
  author_name: "Mickaël CANOUIL, *Ph.D.*"
  author_affiliation: "INSERM U1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille University Hospital, Lille, F-59000, France."
  author_email: ""
  input_files: "/disks/RUN/Array/Dmap/plink/..."
  output_directory: !r here::here("outputs", "03-qc_plink")
  cohort_name: !r params[["project_name"]]
  array: "Illumina Omni2.5"
  callrate_samples: 0.90
  callrate_snps: 0.95
  sex_threshold: !r c(0.2, 0.8)
  heterozygosity_threshold: 4
  maf_threshold: 0.01
  hwe_pvalue: 0.0001
  includes_relatives: FALSE
  mendelian_samples: 0.05
  mendelian_snps: 0.1
  ibd_threshold: 0.2
  population: NULL
  pca_components: 10
  pca_threshold: 3
  max_labels: 15
  check_bim_script: !r system.file("perl", "HRC-1000G-check-bim-NoReadKey.pl", package = "dgapaq")
  imputation_ref: "1KG"
  imputation_panel: "/disks/DATA/ExternalData/1kg/hg19/Reference_genome/1000GP_Phase3_combined.legend"
  ref1kg_panel: "/disks/DATA/ExternalData/1kg/samples_description/integrated_call_samples_v3.20130502.ALL.panel"
  ref1kg_fasta: "/disks/DATA/ExternalData/1kg/hg19/human_g1k_v37.fasta"
  ref1kg_population: "/disks/DATA/ExternalData/1kg/samples_description/1kg_pop_description.tsv"
  ref1kg_genotypes: "/disks/DATA/ExternalData/1kg/hg19/Genotypes/RawPLINK/ALL/"
  bin_path: !r list(bcftools = "/usr/bin/bcftools", bgzip = "/usr/bin/bgzip", plink = "/usr/bin/plink1.9", gcta = "/usr/bin/gcta64")
title: '`r params[["title"]]`'
author:
- name: '`r params[["author_name"]]`'
  affiliation: '`r params[["author_affiliation"]]`'
  email: '`r params[["author_email"]]`'
date: '`r format(Sys.time(), "%B %d, %Y")`'
output:
  bookdown::html_document2:
    theme: simplex
    toc: true
    toc_depth: 3
    toc_float:
      collapsed: false
    fig_width: 6.3
    fig_height: 4.7
    number_sections: true
    self_contained: true
---

<!-- https://github.com/umr1283/dgapaq -->