Variant calling without matched normal sample I have WGS .bam files for 3 patients (tumour and its matched derived model namely organoid) but I don't matched normal sample. If I call variants of each patients (tumour and its matched organoid), how I can use read counts at germline heterozygous positions estimated by GATK 3.2-2 to compensate for the absence of matched normal sample? I heard people use dbsnp VCF instead of the matched normal small variant VCF. But, I don't know start from where? which GATK function does that?


  I should mention, Calling SNV and indel in many tools returns vcf but
  I called copy number by varscan that did not return .vcf output so I
  am not sure what to do for CNV


Any helps please?
If you just want to filter out calls present in dbSNP then use:

java -jar GenomeAnalysisTK.jar \
   -T SelectVariants \
   -R reference.fasta \
   -V patient.vcf \
   --discordance dbSNP.vcf \
   -o patient.filtered.vcf


--discordance will produce calls not present in dbSNP.