Question: GATK HaplotypeCaller with strange genotype conc. results
0
gravatar for szuszmok
3.9 years ago by
szuszmok40
Hungary
szuszmok40 wrote:

Hi All,

I performed a variant caller comparison, and the genotype concordance analysis of HaplotypeCaller's results a little strange to me, and I can't understand it at all.

ALLELES_MATCH:  0  EVAL_SUPERSET_TRUTH:  2438   EVAL_SUBSET_TRUTH: 0   ALLELES_DO_NOT_MATCH: 636   EVAL_ONLY: 20    TRUTH_ONLY:  1014546  

The last and first value could be true? Or anyone can tell what could cause this? I got very different (and reasonable) results e.g. with samtools.

 

Many thanks!

 

snp variant calling • 1.1k views
ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by szuszmok40
2

You will have better luck if you post your question on GATK forum. They are very active over there and you will definitely get some feed back.

ADD REPLYlink written 3.9 years ago by arnstrm1.7k
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