high call rate chrY snps observed in genome studio are not retained in qc'ed genotype data

NCI-CGR / GwasQcPipeline

The CGR GWAS QC processing workflow.

https://nci-cgr.github.io/GwasQcPipeline/

MIT License

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high call rate chrY snps observed in genome studio are not retained in qc'ed genotype data #308

Closed 1teaspoon closed 2 weeks ago

1teaspoon commented 3 months ago

We observed none chrY snps were retained in delivery/subjects.fam However we also observed at least 1000 snps have very good clustering and call rate in genome studio

carynwillis commented 3 months ago

I have confirmed the ChrY (Chr 24 in Plink)snps are in the pre-QC'd sample level plink files (sample_level/samples.bim) but are not in delivery/subjects.bim. I will look into where these snps are being dropped.