Tagged with #somaticindeldetector
0 documentation articles | 0 events or announcements | 3 forum discussions

There are 2 comments on this article. To see them or add your own, read this post on the forum

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?

There are 2 comments on this article. To see them or add your own, read this post on the forum

There are 4 comments on this article. To see them or add your own, read this post on the forum

Hi

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

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

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

There are 4 comments on this article. To see them or add your own, read this post on the forum

There are 4 comments on this article. To see them or add your own, read this post on the forum

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

There are 4 comments on this article. To see them or add your own, read this post on the forum