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"'
Hi there, According to your experience, what do you suggest for calling variants in tumor samples (exome) - HaplotypeCaller or UnifiedGenotyper? Have you seen any (major or minor) difference with both the callers on same exome tumor samples? What's your advice. Do you have any reference publication(s) where HaplotypeCaller is used on tumor samples? Thanks Raj