Question: (Closed) How To Interpret contig field Fields In Vcf Files From 1000 Genomes?
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gravatar for 2012secondseason
14 months ago by
2012secondseason10 wrote:

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.)

breakpoint contig vcf • 478 views
ADD COMMENTlink modified 14 months ago by Pierre Lindenbaum120k • written 14 months ago by 2012secondseason10
0
gravatar for Pierre Lindenbaum
14 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

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?

ADD COMMENTlink modified 14 months ago • written 14 months ago by Pierre Lindenbaum120k
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