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# error using somatic indel detector

Member Posts: 2
edited January 2013

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

##### ERROR ------------------------------------------------------------------------------------------

thanks

Post edited by Geraldine_VdAuwera on
Tagged:

This is addressed in the documentation on this forum. The error you posted specifically asks you not to post this problem to the forum because it's something you can easily fix just by reading the docs that our team has spent a lot of time preparing.

Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

• Member Posts: 6

FYI, that link redirects to the main GATK site, and there does not seem to be any way to find the wiki entry that contains the documentation.

We changed from the wiki to this website, but old versions of the code still produce old links.

FYI, what you're looking for is the first link you get if you use the search box with the terms "ReplaceReadGroups"...

Geraldine Van der Auwera, PhD

• Member Posts: 6

Thanks, Geraldine. (FWIW, I'm not having the problem mentioned above--was just pointing out that the solution was not at the link given to the OP).