What is URL of Contig in VCF format?

Question

[2012secondseason]

Hi..
I am very confused with contig's url.

I know that contig means combination of sample's continuing & overlapping regional reads, but why 'URL' is in Contig's field? That url means what?

1.2.7 Contig field format
As with chromosomal sequences it is highly recommended (but not required) that the header include tags describing the contigs referred to in the VCF file. This furthermore allows these contigs to come from different files. The format is identical to that of a reference sequence, but with an additional URL tag to indicate where that sequence can be found. For example:.

##contig=ID=<ctg1,URL=<a href="&lt;a href=" ftp:="" somewhere.org="" assembly.fa"="" rel="nofollow">ftp://somewhere.org/assembly.fa" rel="nofollow">ftp://somewhere.org/assembly.fa,...>

Help me ,please.
Thank you.

[Devon Ryan]

For those wondering, the formatting of the example is correct in the post but being screwed up during rendering for some reason.

[Ram]

It's the <> signs. They're messing it up.

[Ram]

I've opened an issue on GitHub here: https://github.com/biostars/biostar-engine/issues/231

Answer 1

[Devon Ryan]

The URL is where one can download the reference sequence. You'll see that in other formats too, such as CRAM.

[2012secondseason]

Thanks. But why is reference sequence's url there?? What is the relation between contig and reference sequence?

[Devon Ryan]

It's the sequence of the contig.