Hello
I need some suggestions in filtering the variants in the exome data. I combined all the GVCF files as one file and did joint call genotyping and created one vcf file. The variants in the file were hard-filtered. As first step to evaluate the filtering step, I ran GATK concordance with truth and evaluation data sets and obtained only false negatives. There were no true positives, true negatives and false positives. I created the intervals to be evaluated from the sample vcf file (which was given as evaluation data) and ran the GATK concordance analysis. I am not sure, why the summary results has only false negatives for SNPs and Indels. What could be possibly go wrong?. Can interval list be created from the sample vcf file? If not, how can I create an interval list, if I have don't have one?
Thanks
Priya
