Question: Variant Calling problem - find alternate heterozygous
1
gravatar for Paul
2.3 years ago by
Paul1.3k
European Union
Paul1.3k wrote:

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.

ADD COMMENTlink modified 2.3 years ago by Zaag720 • written 2.3 years ago by Paul1.3k
3
gravatar for Zaag
2.3 years ago by
Zaag720
Amsterdam
Zaag720 wrote:

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

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Zaag720

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...?

ADD REPLYlink written 2.3 years ago by Paul1.3k

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

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Zaag720
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