Tagged with #somaticindeldetector
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Created 2015-02-09 08:06:01 | Updated | Tags: somaticindeldetector

Comments (2)

does GATK V3.3 has some augments which are similar in function in somaticindeldetector, such as:

  1. "-bed" this augment can generate a file in bed format( chr start_pos end_pos), which enable us to directly get the start and end position of an indel. for example: chr15 20000127 20000128 -G:33/81

  2. an augment which tells GATK to call indel only

Created 2014-02-03 02:06:32 | Updated | Tags: somaticindeldetector

Comments (3)

I have run SomaticIndelDetector using following parameters -T SomaticIndelDetector -R ucsc.hg19.fasta -I:normal normal.bam -I:tumor tumor.bam -o sid.vcf -verbose sid.verbose.output

the version of cancer analysis package is 2014.1-13-g6b71cb4 and the gatk version is 2.8.1-2-gaa2d8ac

the input bam files are output from GATK PrintReads(BQSR), and the java run time error happend. Below is the error stack

ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: -1 at org.broadinstitute.sting.utils.collections.CircularArray.get(CircularArray.java:111) at org.broadinstitute.sting.gatk.walkers.indels.SomaticIndelDetector$WindowContext.shift(SomaticIndelDetector.java:1980) at org.broadinstitute.sting.gatk.walkers.indels.SomaticIndelDetector.emit_somatic(SomaticIndelDetector.java:997) at org.broadinstitute.sting.gatk.walkers.indels.SomaticIndelDetector.map(SomaticIndelDetector.java:583) at org.broadinstitute.sting.gatk.walkers.indels.SomaticIndelDetector.map(SomaticIndelDetector.java:134) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:228) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:216) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:102) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:108) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:119) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:92)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2014.1-2.8.1-2-gaa2d8ac):
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.

Is this a bug of SomaticIndelDetector? Will someone please help?

Created 2013-08-28 20:33:57 | Updated 2013-08-28 20:38:22 | Tags: somaticindeldetector

Comments (2)


I am trying to explain a missed INDEL call with SomaticIndelDetector. It is a pretty obvious call. There are plenty of reads to support it, qualities are good etc. Plus I am running with very permissive settings (--filter_expressions T_COV<5||N_COV<5||T_INDEL_F<0.02||T_INDEL_CF<0.1).

No matter what I try though, the caller does not catch the deletion. Is there any way to get further explanaion for something like this or do I just have to put it in the idiosyncrasy bracket?

Created 2013-03-29 18:20:39 | Updated | Tags: somaticindeldetector

Comments (6)


I am using the latest version of GATK 2.4.9 and i don't find the Somatic Indel Detector walker java -jar GenomeAnalysisTK.jar -T SomaticIndelDetector -h

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.4-9-g532efad):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: SomaticIndelDetector
ERROR ------------------------------------------------------------------------------------------

Is this walker is not supported any more.

Thanks Saurabh

Created 2012-09-04 22:27:10 | Updated 2013-01-07 20:41:31 | Tags: somaticindeldetector readgroup

Comments (4)

hello every one please i got this error while running this command

elendin@elendin-HP-Pavilion-dv6700-Notebook-PC:~/analysis of rnaseq bamfiles$ java -jar GenomeAnalysisTK.jar -R VitisVinifera.fasta -T SomaticIndelDetector -o indels.vcf -verbose indels.txt -I:normal wt.bam -I:tumor newmut.bam

MESSAGE: SAM/BAM file SAMFileReader{/home/elendin/analysis of rnaseq bamfiles/newmut.bam} is malformed: Read HWI-ST132_0461:3:2201:1211:140854#GTCCTA is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK. Please use http://www.broadinstitute.org/gsa/wiki/index.php/ReplaceReadGroups to fix this problem

ERROR ------------------------------------------------------------------------------------------

how can i add the missing read group for HWI-ST132_0461:3:2201:1211:140854#GTCCTA or define it in the header. thanks

Created 2012-07-26 15:50:47 | Updated 2012-07-26 17:45:16 | Tags: somaticindeldetector

Comments (2)

Dear developers,

in the recent Cell paper by Hodis et al (Broad Institute) using GATK for somatic mutation calling, authors report filtering indels that were "supported by reads with a high average number of additional mismatches and calls made in genomic loci covered by reads with a high average mismatch rate and low base quality". It is pointed out in the paper that this is a part of GATK. I haven't been able to locate the corresponding algorithm. Could you please point me to the walker/function?