Question: (Closed) How To Interpret contig field Fields In Vcf Files From 1000 Genomes?
gravatar for 2012secondseason
2.1 years ago by
2012secondseason20 wrote:


There are 3 contigs about chromosome 1 in a 1000 genome indels vcf file.(1000G_phase1.indels.hg19.vcf)




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 • 927 views
ADD COMMENTlink modified 2.1 years ago by Pierre Lindenbaum128k • written 2.1 years ago by 2012secondseason20
gravatar for Pierre Lindenbaum
2.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum128k wrote:

it's the dictionary, it's defined in the VCF spec :

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

see also What Do Chromosome Codes Such As 'Chr_Random' Represent?

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Pierre Lindenbaum128k
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