Question: How does one determine whether a deletion is homogeneous or heterogeneous by reading a vcf file with genotype information?
0
gravatar for zhangz.cs
6.2 years ago by
zhangz.cs230
China
zhangz.cs230 wrote:

I got the file union.2010_06.deletions.genotypes.vcf.gz at the 1000genomes ftp site. What information in the file can help me which deletions are homogeneous and which are heterogeneous? Thank for your help in advance.

The beginning of the file header is as follows:

##fileformat=VCFv4.0
##ALT=<ID=DEL,Description="Deletion">
##FILTER=<ID=LowQual,Description="Genotype call confidence below LOD 1.3">
##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">

[...]

sequence next-gen • 2.2k views
ADD COMMENTlink modified 6.2 years ago by Leonor Palmeira3.7k • written 6.2 years ago by zhangz.cs230
2
gravatar for Leonor Palmeira
6.2 years ago by
Leonor Palmeira3.7k
Liège, Belgium
Leonor Palmeira3.7k wrote:

The header from your VCF states that it's in the VCF format version 4.0, so this should get you started:

http://www.1000genomes.org/node/101

(I am deleting the rest of your header, as it doesn't add any information concerning your question)

ADD COMMENTlink modified 6 months ago by RamRS27k • written 6.2 years ago by Leonor Palmeira3.7k

To expand a bit, you want to look at the Genotype (GT) field for each sample of interest. This GATK resource provides a more detailed explanation: http://gatkforums.broadinstitute.org/discussion/1268/how-should-i-interpret-vcf-files-produced-by-the-gatk

ADD REPLYlink written 6.2 years ago by Brad Chapman9.5k
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