Question: Possible SNP combinations and 012 mapping
1
gravatar for rakinhaider
4.0 years ago by
rakinhaider10
rakinhaider10 wrote:

Hello,

I am new to bioinformatics. I am learning about SNPs and trying to use vcftool. In vcftool if i use the --012 option it generates a .012 file with 0,1,2 in it. Where "Genotypes are represented as 0, 1 and 2, where the number represent that number of non-reference alleles."(Ref: Vcftool manual). So If for a snp position the reference allele is C the possible combinations are CC,CT,TC,TT where CC=0, CT/TC=1, TT=2 are the encodings.

My first question is what does this CC mean ?? Does this mean at the particular position there is neocleotide C and it is paring with another neocleotide C on the other strand?

If that so it is not following the base-pair rule . Is it ?

Finally the generated files have very large number of 0's and 2's than that of number of 1's. Should not CT/TC be the common combination that CC and TT.

If I am understanding completely wrong some helpful links will be appreciated.

Thanks In Advance.

snp vcftool • 1.8k views
ADD COMMENTlink modified 4.0 years ago by Devon Ryan96k • written 4.0 years ago by rakinhaider10
2
gravatar for Devon Ryan
4.0 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

CC means homozygous for C. CT/TC would mean heterozygous and so on.

ADD COMMENTlink written 4.0 years ago by Devon Ryan96k
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