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.