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write-index does not appear to work from concat command #2246
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I see what it is doing. In this case it is writing out the VCF in the simplest way ( I will look at making it work. |
This was referenced Sep 18, 2024
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I was concatting 29 uncompressed vcfs and indexing the output
However, the resultant index is more or less empty, and running
bcftools index -n autosomes.vcf.gz
returns 0.Deleting that index and re-indexing (either via
tabix -p vcf
orbcftools index
) produces a larger index that returns the correct number of variants from the previous command.This seems to also occur if the input to concat is compressed, or with
--write-index=tbi
, so seems to be general issue rather than a specific combination of events.This is with
Best,
Alex
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