GATK: RealignerTargetCreator -documentation

[ldh]

I'm looking for some help before using this tool on my data, baby and the bath water etc. Essentially, I'm looking for documentation that describes how this tool determines the locations for realignment. Any help would be greatly appreciated.
Many thanks.
Lee

[vdauwera]

I'm looking for some help before using this tool on my data, baby and the bath water etc. Essentially, I'm looking for documentation that describes how this tool determines the locations for realignment. Any help would be greatly appreciated.
Many thanks.
Lee

See the GATK Best Practices (newly redesigned for clarity) here:

http://www.broadinstitute.org/gatk/guide/best-practices

[binlangman]

RealignerTargetCreator error

When I use GATK to perform local realignment around indels, I run the following command to create a target list of intervals to be realigned firstly:

java -jar /opt/toolkit/GenomeAnalysisTK-2.7-4/GenomeAnalysisTK.jar -T
RealignerTargetCreator -R NC_010473.fasta -I dedup_reads.bam -o target_intervals.list

But there is an error. Here is the error:

INFO 11:12:43,040 HelpFormatter - -------------------------------------------------------------------------------- INFO 11:12:43,043 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-4-g6f46d11, Compiled 2013/10/10 17:27:51 INFO 11:12:43,043 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 11:12:43,043 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 11:12:43,048 HelpFormatter - Program Args: -T RealignerTargetCreator -R NC_010473.fasta -I dedup_reads.bam -o target_intervals.list INFO 11:12:43,049 HelpFormatter - Date/Time: 2013/12/26 11:12:43 INFO 11:12:43,049 HelpFormatter - -------------------------------------------------------------------------------- INFO 11:12:43,049 HelpFormatter - -------------------------------------------------------------------------------- INFO 11:12:43,708 GenomeAnalysisEngine - Strictness is SILENT INFO 11:12:44,116 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 INFO 11:12:44,127 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 11:12:44,145 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 INFO 11:12:44,237 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files INFO 11:12:44,361 GenomeAnalysisEngine - Done preparing for traversal INFO 11:12:44,361 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 11:12:44,361 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining INFO 11:12:48,747 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.7-4-g6f46d11):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: SAM/BAM file SAMFileReader{/home/lmbin/dedup_reads.bam} appears to be using the wrong encoding for quality scores: we encountered an extremely high quality score of 63; please see the GATK --help documentation for options related to this error
ERROR ------------------------------------------------------------------------------------------
I'm a greener, I don't know how to solve the problem in order to finish realignment. Can you give some advice?

[blakeoft]

binlangman,

Is the command that you entered all on one line? Like:

 java -jar /opt/toolkit/GenomeAnalysisTK-2.7-4/GenomeAnalysisTK.jar -T RealignerTargetCreator -R NC_010473.fasta -I dedup_reads.bam -o target_intervals.list

According to http://www.broadinstitute.org/gatk/g...rticle?id=1247 the "--known" argument is required to work properly. However, I'm not sure if omitting it will produce the same error.

[arthurmelo]

I think it's necessary to use the -know option of RealignerTargetCreator. My first attempt to fix this problem was use --fix_misencoded_quality_scores GATK option, but it' not possible. When I use a indels called in a vcf file in -know option the problem was fixed.