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Error in MuTect for mouse models. A newbie !! please help

hns04hns04 Member

Dear Community,
I am a new user trying to detect mutations in my RNA-seq data from mouse models. I have a tumor sample and a normal sample. I downloaded the snp128.txt from UCSC and have the mm9 whole genome with its index and dictionary file all located in the same folder. I did reorder my bam file based on this reference file.
I ran muTect using the standard described by the Broad without the use of intervals though. Still trying to understand that ??.
I get the following output and error :

INFO 17:15:46,353 HelpFormatter - ---------------------------------------------------------------------------------
INFO 17:15:46,355 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.2-25-g2a68eab, Compiled 2012/11/08 10:30:02 INFO 17:15:46,356 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 17:15:46,356 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 17:15:46,361 HelpFormatter - Program Args: --analysis_type MuTect --reference_sequence mm9.fa --dbsnp snp128.txt --input_file:normal Xcc_CD40_IL4.bam --input_file:tumor 1893N_untreated1.bam --out 1893N_untreated_stats.txt --coverage_file 1893N_untreated_coverage.wig.txt INFO 17:15:46,361 HelpFormatter - Date/Time: 2013/06/18 17:15:46 INFO 17:15:46,361 HelpFormatter - ---------------------------------------------------------------------------------
INFO 17:15:46,361 HelpFormatter - ---------------------------------------------------------------------------------
INFO 17:15:47,115 GATKRunReport - Uploaded run statistics report to AWS S3 ##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.2-25-g2a68eab):
##### 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: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types:
##### ERROR Name FeatureType Documentation
##### ERROR BCF2 VariantContext http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_bcf2_BCF2Codec.html
##### ERROR VCF VariantContext http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_vcf_VCFCodec.html
##### ERROR ------------------------------------------------------------------------------------------
****

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