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

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1teaspoon opened this issue Jul 16, 2024 · 1 comment
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high call rate chrY snps observed in genome studio are not retained in qc'ed genotype data #308

1teaspoon opened this issue Jul 16, 2024 · 1 comment
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@carynwillis

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@1teaspoon
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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
@1teaspoon 1teaspoon changed the title chrY snps don't have genotypes after qc pipeline high call rate chrY snps observed in genome studio are not retained in delivery/subjects.fam Jul 16, 2024
@1teaspoon 1teaspoon changed the title high call rate chrY snps observed in genome studio are not retained in delivery/subjects.fam high call rate chrY snps observed in genome studio are not retained in qc'ed genotype data Jul 16, 2024
@carynwillis carynwillis self-assigned this Aug 1, 2024
@carynwillis
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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.

@carynwillis carynwillis mentioned this issue Sep 27, 2024
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@1teaspoon @carynwillis