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meyer-lab-cshl / plinkQC

R package for quality control of plink genetic datasets
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Build version #34

Closed montenegrina closed 3 years ago

montenegrina commented 4 years ago

Describe the bug Can plinkQC run with my plink files which are on Build36 and reference data that is also Build 36. Or do I need to lift both?

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HannahVMeyer commented 3 years ago

The genome build matters for the relatedness estimation as high LD regions are filtered before IBD calculation. The perIndividualQC and check_relatedness functions take the genome build as an input parameter with default genomebuild = "hg19". The help function accessible via check_relatedness offers: 

genomebuild    [character] Name of the genome build of the PLINK file annotations,
                          ie mappings in the name.bim file. Will be used to remove high-LD regions based
                          on the coordinates of the respective build. Options are hg18, hg19 and hg38
HannahVMeyer commented 3 years ago

I am going to close this issue now. Feel free to reopen if still needed/running into issues.