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ContEst without normal.bam
Hello. We only have tumor samples and don't have the paired normal samples. Can we use panel_of_normal.vcf file that mutect2 generated for over 100 normal samples as the genotypes? I tried the following command, but the result is empty. How can I run contEst if I don't have normal sample? Thanks.
java -jar GenomeAnalysisTK.jar \
-T ContEst \
-R hs37d.fa \
-I tumor.bam \
--genotypes Panel_of_normal.vcf \
--popfile hg19_population_stratified_af_hapmap_3.3.FIX.vcf.gz \
-L target.bed \
-isr INTERSECTION -o contamination_out.txt