To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

SNPs Indels seperation from Tumor normal pair

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

Best Answers

Answers

Sign In or Register to comment.