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cggh / scikit-allel

A Python package for exploring and analysing genetic variation data
MIT License
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How to use query atrr of array #355

Open KazegamiKuon opened 3 years ago

KazegamiKuon commented 3 years ago

Hi, I'm currently calculating INDEL and SNP using scikit-allel

I read it as ZARR and make VariantChunkedTable

callset = zarr.open_group(path) variants = allel.VariantChunkedTable(callset.variants)

SNP is where variant have ALT and REF which have only one nucleotide

How can I filter it with 'query'? I checked and see VariantChunkedTable have query atrr variants.query

this is my variants when run code variants = allel.VariantChunkedTable(callset.variants) image

Please advice me on how to process the right format for this function. Thanks