SNPs Indels seperation from Tumor normal pair

suz_katie

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

Geraldine_VdAuwera

Hi there,

GATK is not specifically designed for tumor/normal analysis. Depending on how you have identified your samples, you may be able to do what you want (see documentation for the capabilities of the SelectVariants tool), but there is not one generic command for tumor/normal selections. You may want to look at other software packages related to GATK such as MuTect, which is specifically designed to identify somatic mutations.

http://www.broadinstitute.org/cancer/cga/mutect

Geraldine_VdAuwera

We don't provide the cosmic files in the GATK bundle, but you can ask the MuTect authors in their forum space here: http://gatkforums.broadinstitute.org/categories/mutect

suz_katie

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?