Variant Calling problem - find alternate heterozygous

Question

[Paul]

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.

Answer 1

[Zaag]

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

[Paul]

Thank you Zaag for mention. Probably this kind of caller would be best. Is there any other free solution? Did anybody tested bcftools, varscan, freebayes...?

[Zaag]

bcftools does not work for this, the other ones I've never used