How does one determine whether a deletion is homogeneous or heterogeneous by reading a vcf file with genotype information?
1
0
Entering edit mode
8.1 years ago
zhangz.cs ▴ 280

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">
[...]
next-gen sequence • 2.7k views
ADD COMMENT
2
Entering edit mode
8.1 years ago

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 COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 1141 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6