= Schematic overview of BBMRI/GvNL pipelines =

Input: 
 * Raw read data from BGI 12x (FASTQ)
 * Called variants from BGI (VCF) 
 * Immunochip data


{{{
#!graphviz
digraph G {
BGI->FASTQ->"SNP and indel calling"->VCF
FASTQ->"de novo variant discovery and verification"
BGI->VCF->"Chip QC"->"Qced Genotypes"
ImmunoChip->"Chip QC"
VCF->"Mendelian QC"->"Qced Genotypes"
"Qced Genotypes"->"Call improvement and phasing"->"Improved and phased genotypes"->Imputations
"Improved and phased genotypes"->"Population genetics"
"Improved and phased genotypes"->"Functional variants"
"Improved and phased genotypes"->"Novel variant discovery and verification"
FASTQ->"Novel variant discovery and verification"
}
}}}
}}}