SNPs Indels seperation from Tumor normal pair
Posted in Ask the GATK team | Last updated on


Comments (3)

Hello,

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


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