CompOverlap

CompOverlap is an evaluation module for VariantEval. It computes the following metrics:

Metric	Definition
nEvalSNPs	number of eval SNP sites
nCompSNPs	number of comp SNP sites
novelSites	number of eval sites outside of comp sites
nVariantsAtComp	number of eval sites at comp sites (that is, sharing the same locus as a variant in the comp track, regardless of whether the alternate allele is the same)
compRate	percentage of eval sites at comp sites
nConcordant	number of concordant sites (that is, for the sites that share the same locus as a variant in the comp track, those that have the same alternate allele)
concordantRate	the concordance rate

Understanding the output of CompOverlap

A SNP in the detection set is said to be 'concordant' if the position exactly matches an entry in dbSNP and the allele is the same. To understand this and other output of CompOverlap, we shall examine a detailed example. First, consider a fake dbSNP file (headers are suppressed so that one can see the important things):

$ grep -v '##' dbsnp.vcf
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
1       10327   rs112750067     T       C       .       .       ASP;R5;VC=SNP;VP=050000020005000000000100;WGT=1;dbSNPBuildID=132

Now, a detection set file with a single sample, where the variant allele is the same as listed in dbSNP:

$ grep -v '##' eval_correct_allele.vcf
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT            001-6
1       10327   .       T       C       5168.52 PASS    ...     GT:AD:DP:GQ:PL    0/1:357,238:373:99:3959,0,4059

Finally, a detection set file with a single sample, but the alternate allele differs from that in dbSNP:

$ grep -v '##' eval_incorrect_allele.vcf
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT            001-6
1       10327   .       T       A       5168.52 PASS    ...     GT:AD:DP:GQ:PL    0/1:357,238:373:99:3959,0,4059

Running VariantEval with just the CompOverlap module:

$ java -jar $STING_DIR/dist/GenomeAnalysisTK.jar -T VariantEval \
       -R /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta \
       -L 1:10327 \
       -B:dbsnp,VCF dbsnp.vcf \
       -B:eval_correct_allele,VCF eval_correct_allele.vcf \
       -B:eval_incorrect_allele,VCF eval_incorrect_allele.vcf \
       -noEV \
       -EV CompOverlap \
       -o eval.table

We find that the eval.table file contains the following:

$ grep -v '##' eval.table | column -t 
CompOverlap  CompRod  EvalRod                JexlExpression  Novelty  nEvalVariants  nCompVariants  novelSites  nVariantsAtComp  compRate      nConcordant  concordantRate
CompOverlap  dbsnp    eval_correct_allele    none            all      1              1              0           1                100.00000000  1            100.00000000
CompOverlap  dbsnp    eval_correct_allele    none            known    1              1              0           1                100.00000000  1            100.00000000
CompOverlap  dbsnp    eval_correct_allele    none            novel    0              0              0           0                0.00000000    0            0.00000000
CompOverlap  dbsnp    eval_incorrect_allele  none            all      1              1              0           1                100.00000000  0            0.00000000
CompOverlap  dbsnp    eval_incorrect_allele  none            known    1              1              0           1                100.00000000  0            0.00000000
CompOverlap  dbsnp    eval_incorrect_allele  none            novel    0              0              0           0                0.00000000    0            0.00000000

As you can see, the detection set variant was listed under nVariantsAtComp (meaning the variant was seen at a position listed in dbSNP), but only the eval_correct_allele dataset is shown to be concordant at that site, because the allele listed in this dataset and dbSNP match.