ERROR report about the Mutect1.1.7

[MenglinC]

Dear professors @dinvlad,

These days I use the Mutect1.1.7 to call the SNVs in my project!However,I come across the errors that listed as follows.I have searched many places in the website,but haven't found any clear explanations about it!So,I list them here,and hope to get some suggestions!

• error message

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 (this is an external codec and is not documented within GATK)
ERROR VCF VariantContext (this is an external codec and is not documented within GATK)
ERROR VCF3 VariantContext (this is an external codec and is not documented within GATK)

• code line
  /home/xxzhang/workplace/software/java/jdk1.7.0_80/bin/java -Djava.io.tmpdir=./output_RNA/mutmp -Xmx31g -jar /home/xxzhang/workplace/QBRC//somatic_script/mutect-1.1.7.jar --analysis_type MuTect --reference_sequence ./geneome/hg19/hg19.fa --dbsnp ./geneome/hg19/hg19.fa_resource/dbsnp.hg19.vcf --cosmic ./geneome/hg19/hg19.fa_resource/CosmicCodingMuts.hg19.vcf --input_file:tumor /home/xxzhang/workplace/QBRC/output_RNA/tumor/tumor.bam --input_file:normal /home/xxzhang/workplace/QBRC/output_RNA/normal/normal.bam --vcf ./output_RNA/mutect.vcf --out ./output_RNA/mutect.out

• the help document about the mutect

Available Reference Ordered Data types:
Name FeatureType Documentation
BCF2 VariantContext (this is an external codec and is not documented within GATK)
BEAGLE BeagleFeature http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_beagle_BeagleCodec.html
BED BEDFeature (this is an external codec and is not documented within GATK)
BEDTABLE TableFeature http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_table_BedTableCodec.html
EXAMPLEBINARY Feature (this is an external codec and is not documented within GATK)
GELITEXT GeliTextFeature (this is an external codec and is not documented within GATK)
OLDDBSNP OldDbSNPFeature (this is an external codec and is not documented within GATK)
RAWHAPMAP RawHapMapFeature http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_hapmap_RawHapMapCodec.html
REFSEQ RefSeqFeature http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_refseq_RefSeqCodec.html
SAMPILEUP SAMPileupFeature http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_sampileup_SAMPileupCodec.html
SAMREAD SAMReadFeature http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_samread_SAMReadCodec.html
TABLE TableFeature http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_table_TableCodec.html
VCF VariantContext (this is an external codec and is not documented within GATK)
VCF3 VariantContext (this is an external codec and is not documented within GATK)

Does the problem is that this is an external codec and is not documented within GATK about the BCF2/VCF/VCF3,and I need to add them in my workplace!

Thanks very much!