Dear all,

lets assume we have reference genome and its mapped reads:

    ref:     ACGTCTTCGTCAATG
    read1:   ACGA
    read2:   ACGA
    read3:   ACGC
    read4:   ACGC

my variant caller should generate something like: **het A/C - 50%**. Dou you have any experiences with this calling? What caller can handle this problem? I found that some callers just skip this site.

Best,

Paul.
GATK's HaplotypeCaller would call this:


    | CHROM | POS      | REF | ALT | GT   |
    |-------|----------|-----|-----|------|
    | chr   | 1        | T   | A,C |  1/2 |



So for GT the ref (T) is 0, the first alternate (A) is 1 and the second (C) is 2, so

TT = 0/0 = WT

AA = 1/1 = Homozygous variant first alternate 

CC = 2/2 = Homozygous variant  and the second alternate 

TA = 0/1 = Heterozygote with REF and first alternate allele

TC = 0/2 = Heterozygote with REF and second alternate allele

and what you described above:

A/C = 1/2 = Heterozygote with both alternate alleles

