I'd like to know if someone has tested the concordance from output of PhaseByTransmission with SNP array data.
I have calculated the genotype concordance for the most likely GT combination from the VCF obtained from unified genotyper for a family trio based on the GL values against SNP array data and then did the same for the genotypes obtained after using PhaseByTransmission and I'm seeing a drop in concordance.
Is this to be expected?
I have the following problem:
I am evaluating genotype concordance using:
-T VariantEval --evalModule GenotypeConcordance -comp ref.vcf -eval sample1.observed.vcf
If I use a reference genotype file with multiple samples in it where one of the genotype columns is NA1234 (the sample in question), then the sensitivity for all SNP types (HOM_REF,HET,HOM_VAR) decreases drastically. This is because the GATK gets confused when there is more than one sample in the reference file. I know this because if I use a reference genotype file (ref.vcf) with only a single hapmap sample (NA1234) everything works fine and sensitivity is good. So this is not a detection problem is a problem when SNPs are being compared against the reference.
I tried passing the sample name using the --sample parameter for -T VariantEval, but this does not work either (sensitivity is still way off).
In previous versions of the GATK this was done automatically where genotypes where compared based on the sample name within the detection vcf file (sample1.observed.vcf ) vs the ref.vcf file without having to specify the sample name explicitly.
How can I avoid this problem? I want to have a master reference genotype file with multiple samples that I can use for different samples.
I am using GATK version v1.6
Thank you, Gene
I'm looking to find all the entries that change between two calls to UG on the same data. I would like to find all the entries where the call in the variant tract are different from those in the comparison track. So in effect I want those entries that would not be result from -using -conc in SelectVariants. From the documentation is is unclear if the -disc option does this:
A site is considered discordant if there exists some sample in the variant track that has a non-reference genotype and either the site isn't present in this track, the sample isn't present in this track, or the sample is called reference in this track.
What if the comp is HOM_VAR and the variant track is HET? Or if they are both HET but disagree on the specific allele?
I am using VariantEval --evalModule GenotypeConcordance in order to establish concordance and sensitivity metrics against a HapMap reference. In the resulting GATK report I obtain the following fields for a given SNP category (example with HETs):
GenotypeConcordance CompRod EvalRod JexlExpression Novelty variable value--- GenotypeConcordance comp eval none all n_true_HET_called_HET 6220 GenotypeConcordance comp eval none all n_true_HET_called_HOM_REF 0 GenotypeConcordance comp eval none all n_true_HET_called_HOM_VAR 20 GenotypeConcordance comp eval none all n_true_HET_called_MIXED 0 GenotypeConcordance comp eval none all n_true_HET_called_NO_CALL 318 GenotypeConcordance comp eval none all n_true_HET_called_UNAVAILABLE 0
What is the meaning of the _MIXED and _UNAVAILABLE fields?
Just to make sure my understanding is correct:
HET: heterozygous HOM_REF: homozygous reference HOM_VAR: homozygous variant MIXED: something like `./1` Mismatching_Alleles: ?? UNAVAILABLE: for internal use ALLELES_MATCH: ?? ALLELES_DO_NOT_MATCH: ?? EVAL_ONLY: ?? TRUTH_ONLY: does it actually mean the variants present in comp but not in eval, like COMP_ONLY?
how does the following computed?
Non-Reference_Discrepancy Non-Reference_Sensitivity Overall_Genotype_Concordance
Thanks a lot!
I would like to evaluate variant calls to produce a plot (psuedo-ROC) of sensitivity vs. specificity (or concordance, etc) when I condition on a minimum/maximum value for a particular metric (coverage, genotype quality, etc.). I can do this by running VariantEval or GenotypeConcordance multiple times, once for each cutoff value, but this is inefficient, since I believe I should be able to compute these values in one pass. Alternatively, if there was a simple tool to annotate each variant as concordance or discordant, I could tabulate the results myself. I would like to rely upon GATK's variant comparison logic to compare variants (especially indels). Any thoughts on if current tools can be parameterized, or adapted for these purposes?
Thanks for your help in advance,