Hi friends,

Anyone have any similar experience about the duplicated allele with different allele frequency.

My example is as below: chr20 xxxxxx N N 0 28 52.83% 0 2 0 26 1.3074133236616653E-16 0 1 0 0 13 15 C chr20 xxxxxx N N 0 25 47.17% 0 2 0 29 7.910728602448565E-15 0 1 0 0 12 13 C

We have three questions: 1, how to get the right reference allele, not "N". We checked the genome file, it is not "N". 2, We have the variants in the same position in another sample, the most frequent non-reference alleles "T". We found these two duplicated results may be wrong, one is "T", not "C". How can varscan produce the duplicated variants with different allele frequency, is it possible varscan have a bug. 3, How can we convert the text file to vcf file or input file for annovar annotation.

Thanks a lot,