Question: 1000 genomes genotypes interpretation
0
gravatar for cocchi.e89
5 weeks ago by
cocchi.e8920
cocchi.e8920 wrote:

Dear all, I am working on some variants and comparing them with 1000 genomes data. I would like to retrive the number of homozigote patients for the variant, the 1000g VCF file looks like a long list of 0|0 (or 1/2). I looked at their website (http://www.internationalgenome.org/category/genotypes/) but it is still unclear to me, how would a ALT HOM be specified? And an ALT HEM? What is the difference between 0|1 and 0|2 for example.

Thanks a lot in advance for any help!

het genotype hom 1000g • 94 views
ADD COMMENTlink written 5 weeks ago by cocchi.e8920
2
gravatar for Pierre Lindenbaum
5 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

VCF specification https://samtools.github.io/hts-specs/VCFv4.2.pdf . section 1.4.2 "genotype fields"

ADD COMMENTlink written 5 weeks ago by Pierre Lindenbaum120k
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