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">
[...]
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zhangz.cs •
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)
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written
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Leonor Palmeira
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
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