Hello.
There are 3 contigs about chromosome 1 in a 1000 genome indels vcf file.(1000G_phase1.indels.hg19.vcf)
contig=<id=chr1,length=249250621,assembly=hg19>
contig=<id=chr1_gl000191_random,length=106433,assembly=hg19>
contig=<id=chr1_gl000192_random,length=547496,assembly=hg19>
I dont understand what 'assembly' exactly means. In fact, I don't fully understand how breakpoint are assembled.
contig, breakpoint, indel, assembly. How they are related?? :( If you explain it with picture I would be so grateful. (Any answer would be helpful.)
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2012secondseason •
1 answer
it's the dictionary, it's defined in the VCF spec : https://samtools.github.io/hts-specs/VCFv4.2.pdf
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
assembly is human genome version hg19 https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19
see also What Do Chromosome Codes Such As 'Chr_Random' Represent?
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