= SOP for converting LifeLines Geno Data  =

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This SOP applies to LL3.

Data is released to researcher 'per study' (i.e. an approved research request). 
* Per study a subset of the genotypes is created and made available to the researcher:
* Only individuals selected for study (e.g. 5000 out of total 17000)
* The identifiers 're-pseunomized' from 'marcel identifiers' to 'study identifiers' (so data can not be matched between studies).

== Expected outputs ==

User expects files in PLINK format:
* TPED/TFAM genotype files (chosen for internal use as easier to produce)
* BIM/BED/FAM genotype files (with empty phenotype, monomorphic filtered)
* BIM/BED/FAM genotype files splitted per chromosome
* MAP/PED '''dosage''' files
* MAP/PED dosage files '''splitted per chromosome'''

== Available inputs ==

Complete genotype data is in: /target/gpfs2/lifelines_rp/releases/LL3/