Question: What is URL of Contig in VCF format?
0
gravatar for 2012secondseason
19 months ago by
2012secondseason20 wrote:

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.

contig • 603 views
ADD COMMENTlink modified 19 months ago by RamRS24k • written 19 months ago by 2012secondseason20
1

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

ADD REPLYlink written 19 months ago by Devon Ryan92k
1

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

ADD REPLYlink written 19 months ago by RamRS24k

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

ADD REPLYlink written 19 months ago by RamRS24k
4
gravatar for Devon Ryan
19 months ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

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

ADD COMMENTlink written 19 months ago by Devon Ryan92k

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

ADD REPLYlink written 19 months ago by 2012secondseason20

It's the sequence of the contig.

ADD REPLYlink written 19 months ago by Devon Ryan92k
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