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I'm using ContEst for quantification of sample contamination and the commandline used is as follows:
java -Xmx2400m -jar /contest-1.0.24530-bin/ContEst.jar \
-T Contamination \
-I Sample1.bam \
-R hg19.fa \
-B:pop,vcf hg19_hapmap.vcf \
-B:genotypes,vcf Sample1.vcf \
-BTI genotypes \
-L Target.bed \
It generated an output:
_name population population_fit contamination confidence_interval_95_width confidence_interval_95_low confidence_interval_95_high sites
META CEU n/a 0.1 0.1 0.1 0.2 1742
and the contamination is 0.1% (and also for other samples as well), which seems unrealistic, as I'm expecting around 10%,