Question: Difficulty in using GATK for SNP and indel analysis
1
gravatar for jamessemaj712
3.2 years ago by
jamessemaj71210 wrote:

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.

snp gatk indel • 1.3k views
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by jamessemaj71210

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

ADD REPLYlink written 3.2 years ago by jamessemaj71210
1

Glad to help and good luck.

Upvoting our answer will make us happy ;)

ADD REPLYlink written 3.2 years ago by WouterDeCoster39k
2
gravatar for WouterDeCoster
3.2 years ago by
Belgium
WouterDeCoster39k wrote:

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

ADD COMMENTlink written 3.2 years ago by WouterDeCoster39k
1
gravatar for igor
3.2 years ago by
igor7.6k
United States
igor7.6k wrote:

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.

ADD COMMENTlink written 3.2 years ago by igor7.6k
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