Difficulty in using GATK for SNP and indel analysis

Question

[jamessemaj712]

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.

[jamessemaj712]

Thanks decosterwouter and igor.I read best practices,I am getting the confidence to proceed further.

[WouterDeCoster]

Glad to help and good luck.

Upvoting our answer will make us happy ;)

Answer 1

[WouterDeCoster]

There is a step by step guide: GATK best practices https://www.broadinstitute.org/gatk/guide/best-practices.php

Answer 2

[igor]

Realignment is a two-step process using RealignerTargetCreator and then IndelRealigner. See detailed instructions here: https://www.broadinstitute.org/gatk/guide/article?id=38

The rest of the best practices tutorial will be helpful too.