I'm starting to use GATK tool and I've two general questions (sorry if they are basic but I can not find the correct way to proceed).
I've aligned 10 bam files of different samples against human_g1k_v37.fasta genome. Now I want to perform "RealignerTargetCreator" and "IndelRealigner" steps in order to get as good as possible variant calling results. Questions:
1) What file should I put in "-known" argument? Mills_and_1000G_gold_standard.indels.b37.vcf or 000G_phase1.indels.b37.vcf (both are available in bundle)? Maybe both? Or I should create my own file?
2) I have to run RealignerTargetCreator for each bam...?
3) IndelRealigner, I have to put the same -known file as in RealignerTargetCreator step?
Thanks in advance for the help.