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SNPs Indels seperation from Tumor normal pair

suz_katiesuz_katie Member Posts: 3


I am using the following command to generate SNPs and Indels from matching tumor normal pair bam files (GenomeAnalysisTK-2.4-9-g532efad)

java -jar GenomeAnalysisTK.jar -glm BOTH -R ucsc.hg19.fasta -T UnifiedGenotyper -I tumor.bam -I normal.bam -D dbsnp_135.hg19.vcf -o raw.snps.indels.vcf -metrics snps.metrics -stand_call_conf 50.0 -stand_emit_conf 10.0.

I would like to know the specific command (in SelectVariants) to separate SNPs unique to tumor but not to normal sample

Best Answers


  • suz_katiesuz_katie Member Posts: 3

    Thanks a lot for your prompt response. where can I find hg19 cosmic files in the bundle for mutect, I can see only dnsnp files and reference genome in the hg19 bundle ( bundle/2.3/hg19/). Am I looking in the wrong directory?

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