If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 126.96.36.199
mutect version used:1.7.0
b) Exact command used: `/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 `
c) Entire error log:
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)
With regard to this error,I have turn to help from the Google website or the mutect github website.
The possible explanation about this problem is :
> I finally figured it out: It was something off the the VariantAnnotator vcf from GATK, I re-ran it and used the new file, I also deleted the old index file. The manual correction of the ESP VCF works! Its a bit boring, but it does the job. Hope this help anyone else getting this error! **Replace all chromosome names manually using "find & replace" in Textedit.** Its something about the formatting thats off.
I check these files in my working environment,but it doesn't work!So,I want to receive the help from you!
Thanks very much!
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