select mutants specific to tumor sample in a tumor/normal pair
I am wondering if it would be okay to use the "SelectVariants" tool to select mutants specific to the tumor sample in a pair of tumor and normal samples. I tried the following command, and it seems working. But I am suspecting whether it differentiates the genotype differences (e.g. 0/1 in tumor sample and 0/0 in normal sample) or coverage differences (e.g. 0/1 in tumor sample and ./. in normal sample).
Could someone help me understand "SelectVariants" for my question? Thanks a lot!
java -Xmx10g -Djava.io.tmpdir=$tempSpillFolder -jar $CLASSPATH/GenomeAnalysisTK.jar \ -R $GenomeReference \ -T SelectVariants \ --variant $file \ -o $OutputFolder/$filename.selected.vcf \ -select 'set=="tumor"'