Check samplesheet for chr prefix

PGScatalog / pgscatalog_utils

(superseded by pygscatalog) Utilities for working with PGS Catalog API and scoring files

Apache License 2.0

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Closed nebfield closed 8 months ago

nebfield commented 10 months ago

VCF input in GRCh38 will be set up like chr1, chr2, ...
plink2 strips chr prefix by default during recoding
we match the samplesheet chr column against the recoded plink data
if there's a mismatch between samplesheet and internal plink files then you can get problems https://github.com/PGScatalog/pgsc_calc/issues/72#issuecomment-1757744700

do we check for chr prefix and error?

nebfield commented 8 months ago

nebfield commented 8 months ago