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MuTect - No tribble type error
I'm trying to run MuTect over paired tumor-normal bam files but I can't get past the following error:
ERROR A USER ERROR has occurred (version 2.2-25-g2a68eab)
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
none of the links actually sends to a working page.
the command line is the following:
java -jar muTect-1.1.4.jar \
--analysis_type MuTect \
--reference_sequence /genomes/hg19_reordered.fa \
--dbsnp dbsnp_138_hg19_reordered.vcf \
--cosmic b37_cosmic_v54_120711_reordered.vcf \
--input_file /ExomeSeq/Normal_sorted_group.bam \
--input_file /ExomeSeq/Tumor_sorted_group.bam \
--out /ExomeSeq/MuTectOutput/calls.txt \
and the "reordered" simply indicates that the chrs are in the order 1-->22,X,Y,M
any help would be golden