Question: (Closed) What is the relation between contig and reference sequence in VCF format?
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gravatar for 2012secondseason
16 months ago by
2012secondseason20 wrote:

As far as I know, Contig is a combination of continuous & overlapping reads. But in description of VCF format, there is a URL of reference in Contig field like this.

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= http://somewhere.org/assembly.fa...>

Why url of reference sequence is in there?? I'm thoroughly confused about relation between contig and reference sequence.

Would you care to elaborate on that a little? Thanks in advance.

reference contig • 313 views
ADD COMMENTlink written 16 months ago by 2012secondseason20

Hello 2012secondseason!

We believe that this post does not fit the main topic of this site.

wy asking a new question ? Devon answered A: What is URL of Contig in VCF format?

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

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ADD REPLYlink written 16 months ago by Pierre Lindenbaum122k
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