Question: Not understand the value in VCF file
gravatar for leovam173
12 months ago by
leovam1730 wrote:

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!

ADD COMMENTlink written 12 months ago by leovam1730

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 REPLYlink written 12 months ago by JC11k

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 REPLYlink written 11 months ago by Torst960
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