VCF File interpreting

Question

[largesoda7]

Hi Guys! I have a simple question you may think but i am pretty new to this kind of section and never worked with stuff like this before so i would appreciate your help. My problem is that i have this snippet from a VCF File and i dont know how to interpret the GT section

SAMPLEID (NA12453,Sex=FEMALE,Affectionstatus=1)
SAMPLEID (NA12451,Sex=MALE,Affectionstatus=0)
SAMPLE (ID=NA12452,Sex=FEMALE,Affectionstatus=0)
PEDIGREE (Father=NA12451,Mother=NA12452,Child=NA12453)
CHROM   POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  NA12451 NA12452 NA12453
1   746775  rs6699990   A   G   .   PASS    AA=N;DP=120 GT:GQ:DP    0|1:100:34   0|0:89:30    0|0:100:46

I think that this means, that the child got the 0allel from his father and the other 0 from his mother. 1) But can you relate that in this case mother and father are the "real" parents from this child? 2) How can u just by looking at this find variations in affected persons with the same genotype, but not in healthy family members or find new mutations considering the heterozygoty

i am really confused right now so i would appreciate any kind of help wish you all the best largesoda

[Pierre Lindenbaum]

• What Does Genetype ("0/0", "0/1" Or "1/1") In *.Vcf File Represent?
• Genotype representation with 0, 1, 2 - what do they mean?
• VCF Files: Help on 0/1 1/1 0/0 1/1 | vs / (phased & unphased

Answer 1

[JC]

Father NA12451 is 0|1, so the call is A/G

Mother NA12452 is 0|0, so the call is A/A

Child (female) NA12453 is 0|0, so the call is A/A

Therefore, the child gets one A from mom and another A from dad.

Then, 1) no evidence unless you have more data, 2) because the calls are reference it could be no-pathogenic