no indel calls
I am using GATK to call SNPs and indels for eight mammal genomes with ~20X coverage and mapping to a reference genome.
I am able to get through the entire pipeline and call both SNPs and indels as directed in the tutorial -- mapping, sorting, RealignerTagetCreator, IndelRealigner, BaseRecalibrator, UnifiedGenotyper (due to processing issues, it will take about a month to run HaplotypeCaller), SelectVariants for SNPs, and SelectVariants for Indels.
I am able to identify plenty of SNPs using this method but my I am coming up empty with the indels. I get a vcf file with the proper headers but the list of indels is empty.
What should I look for to identify the problem? Any help would be appreciated.