Hi,
So I have finally managed to get GATK 1.3 to spit out indels and snps for my exome data. Can someone please share the filters that are reliable. I am hoping to get ti/tv ~ 3.0 and proportion of snps in dbsnp to be ~91% in the targetted coding region. It would be great to see what different people use and what validation success rate they are achieving.
thanks
So I have finally managed to get GATK 1.3 to spit out indels and snps for my exome data. Can someone please share the filters that are reliable. I am hoping to get ti/tv ~ 3.0 and proportion of snps in dbsnp to be ~91% in the targetted coding region. It would be great to see what different people use and what validation success rate they are achieving.
thanks