Not understand the value in VCF file

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5.3 years ago

SkyL ▴ 10

Hi, I am new to sequencing analysis. I got the vcf file and need some help to understand the meaning. In the last two columns, there are some rows like:

GT:CNADJ 0|1:2,

I know 0|1 represent hetero, and CNADJ is the copy number of the adjacency (not sure what it is) but why there is only one number (2) after the colon? I was expecting two numbers like 0|1:2,1.

Also, there are some rows show:

GT:CNADJ 0|1:-1

what does -1 mean here? Thanks very much!

genome SV sequencing copy number • 904 views

ADD COMMENT • link 5.3 years ago by SkyL ▴ 10

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The best way to understand it is to check the documentation from the program which created the file because VCF format can have custom fields.

ADD REPLY • link 5.3 years ago by JC 13k

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This one seems to be in the VCF 4.2 standard:

##INFO=<ID=CNADJ,Number=.,Type=Integer,Description="Copy number of adjacency">

But as you say, the software using it may not be following the rules. Usually something like -1 would be used to mean "no information" or "error".

ADD REPLY • link 5.3 years ago by Torst ▴ 980

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