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


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
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
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 683 users visited in the last hour