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core operationsIssues related to domain-specific functionality such as LD pruning, PCA, association testing, etc.Issues related to domain-specific functionality such as LD pruning, PCA, association testing, etc.
Description
It would be very useful to have the ability to subset a dataset using bcftools
expressions for regions (-r/-t
), filter expressions (-i/-e
), and samples (-s
).
This is now possible using the work we have done in vcztools
, such as sgkit-dev/vcztools#234. In particular, we now have an index that allows efficient region queries (which will address #25).
This will also address #1084.
See an initial prototype in sgkit-dev/bio2zarr#365 (comment)
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core operationsIssues related to domain-specific functionality such as LD pruning, PCA, association testing, etc.Issues related to domain-specific functionality such as LD pruning, PCA, association testing, etc.