Hi,

I am new to Bioinformatics.I am trying to use GATK tool for finding SNP and indels but the problem is that the documentation seems to be complex for a beginner like me with so many tools to start with including IndelRealigner,MuTect,Haplotypecaller..The more I read the more confused I am getting.I also tried using Indel religner which is the first step in the process of identification of indels(correct me if wrong) but I got  an error saying that you don't have the intervals file in the targetIntervals in the following command.


 java -jar GenomeAnalysisTK.jar \
   -T IndelRealigner \
   -R reference.fasta \
   -I input.bam \
   -known indels.vcf \
   -targetIntervals intervalListFromRTC.intervals \
   -o realignedBam.bam
 
The error message is:Could not read file /home/aditya/Bioinfotools/gatk/intervalListFromRTC.intervals because The interval file does not exist.
I don't know where to get the intervals file from.

But please guide me overall in understanding GATk.
There is a step by step guide: GATK best practices
https://www.broadinstitute.org/gatk/guide/best-practices.php