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zhengxwen / SeqArray

Data management of large-scale whole-genome sequence variant calls (Development version only)
http://www.bioconductor.org/packages/SeqArray
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Changing genotypes #51

Closed thierrygosselin closed 5 years ago

thierrygosselin commented 5 years ago

The 3D array for “genotype” is presence/absence of REF and ALT alleles coded 0/1, how’s the missing coded? When I use NA it’s not converted to missing.

I can have a reproducible example if it helps

thierrygosselin commented 5 years ago

recoding NA to 0x0F seems to fix my problem...

zhengxwen commented 5 years ago

or recoding NA to -1