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Top-level attribute(s) for assembly information #4

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jeromekelleher opened this issue Nov 3, 2022 · 0 comments
Open

Top-level attribute(s) for assembly information #4

jeromekelleher opened this issue Nov 3, 2022 · 0 comments

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@jeromekelleher
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jeromekelleher commented Nov 3, 2022

I'm not sure how well this is supported in the VCF spec or parsers, but it would be very helpful to present information about the genome assembly.

In practise the useful information will probably be in the contig header, and the actual assembly header won't be much use if it's just referring to a fasta file. The VCF spec gives these examples:

##assembly=url

##contig=<ID=ctg1,length=81195210,URL=ftp://example.com/assembly.fa,md5=f126cdf8a6e0c7f379d618ff66beb2da,...>

I guess all we can do is keep the information about the assembly and contig around as attributes so that they can be easily inspected?

@jeromekelleher jeromekelleher changed the title Top-level attribute for Assembly information Top-level attribute(s) for assembly information Nov 3, 2022
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