= Schematic overview of BBMRI/GvNL pipelines = Input: * Raw read data from BGI 12x (FASTQ) * Called variants from BGI (VCF) * Immunochip data {{{ #!graphviz digraph G { ranksep=.75; size = "10,10"; node[shape=folder] "Biobanks" "Sequence Reads (FASTQ)" "Qced Genotypes (VCF)" "Coverage report" "Improved and phased genotypes" "GWAS control cohorts" "Imputed GWAS control cohorts" "Dutch HapMap" node[shape=diamond, style=filled, fillcolor=yellow] Biobanks->BGI->"Sequence Reads (FASTQ)"->"Alignment"->"SNP and indel calling"->"Chip QC"->"Mendelian QC"->"Qced Genotypes (VCF)" "Alignment"->"Coverage analysis"->"Coverage report" BGI->"Chip QC" Biobanks->ImmunoChip->"Chip QC" "Qced Genotypes (VCF)"->"Call improvement and phasing"->"Improved and phased genotypes"->Imputations Biobanks->"GWAS control cohorts"->Imputations->"Imputed GWAS control cohorts" "Improved and phased genotypes"->"Population genetics"->"Dutch HapMap" "Improved and phased genotypes"->"Functional variants"->"Dutch HapMap" "Improved and phased genotypes"->"Novel variant discovery and verification"->"Dutch HapMap" "Sequence Reads (FASTQ)"->"Novel variant discovery and verification" "Qced Genotypes (VCF)"->TrioAwarePhasing -> "Improved and phased genotypes" } }}}