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missing variant from tabix #109

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nzhun opened this issue Oct 18, 2024 · 0 comments
Open

missing variant from tabix #109

nzhun opened this issue Oct 18, 2024 · 0 comments

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@nzhun
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nzhun commented Oct 18, 2024

My issue is below:
I used tabix 1.21, I use tabix to extract a variant, for example:
tabix s3://pan-ukb-us-east-1/sumstats_flat_files/categorical-20001-both_sexes-1001.tsv.bgz 18:57851097-57851098
tabix return me nothing.
But If I use a larger region,
tabix s3://pan-ukb-us-east-1/sumstats_flat_files/categorical-20001-both_sexes-1001.tsv.bgz 18:57851097-5799979, in the returned list, it has 18:57851097:T:C

When I cp the bgz abd tbi files on the aws on my local computer, it still cannot work with 18:57851097-57851098. But when I indexed the bgz file locally (replace the copied tbi file from s3), I can get the variant using the one base region.

It seems it is a problem of the tbi on AWS S3. can anyone help to confirm it?

thank you

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