Hi!
I am running into an error while running BaseRecaliberator, I also googled it up and tried a lot of suggestion but nothing helped.
Here is what I am doing:
java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R hg19.fa -I Realigned_Mydata.sort.MarkDup.RG.bam -knownSites dbsnp_137.hg19.vcf.done -knownSites Mills_and_1000G_gold_standard.indels.hg19.vcf -o Recal.table_289
The error that I get is
INFO 09:53:40,686 HelpFormatter - --------------------------------------------------------------------------------
INFO 09:53:40,703 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03
INFO 09:53:40,706 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 09:53:40,709 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 09:53:40,746 HelpFormatter - Program Args: -T BaseRecalibrator -R hg19.fa -I Realigned_Mydata.sort.MarkDup.RG.bam -knownSites dbsnp_137.hg19.vcf.done -knownSites Mills_and_1000G_gold_standard.indels.hg19.vcf -o Recal.table_289
INFO 09:53:40,765 HelpFormatter - Executing as abhishek@mb06 on Linux 3.12.21-gentoo-r1 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_55-b13.
INFO 09:53:40,767 HelpFormatter - Date/Time: 2014/08/29 09:53:40
INFO 09:53:40,768 HelpFormatter - --------------------------------------------------------------------------------
INFO 09:53:40,769 HelpFormatter - --------------------------------------------------------------------------------
INFO 09:53:49,753 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.2-2-gec30cee):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### 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 (this is an external codec and is not documented within GATK)
##### ERROR BEAGLE BeagleFeature (this is an external codec and is not documented within GATK)
##### ERROR BED BEDFeature (this is an external codec and is not documented within GATK)
##### ERROR BEDTABLE TableFeature (this is an external codec and is not documented within GATK)
##### ERROR EXAMPLEBINARY Feature (this is an external codec and is not documented within GATK)
##### ERROR GELITEXT GeliTextFeature (this is an external codec and is not documented within GATK)
##### ERROR OLDDBSNP OldDbSNPFeature (this is an external codec and is not documented within GATK)
##### ERROR RAWHAPMAP RawHapMapFeature (this is an external codec and is not documented within GATK)
##### ERROR REFSEQ RefSeqFeature (this is an external codec and is not documented within GATK)
##### ERROR SAMPILEUP SAMPileupFeature (this is an external codec and is not documented within GATK)
##### ERROR SAMREAD SAMReadFeature (this is an external codec and is not documented within GATK)
##### ERROR TABLE TableFeature (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)
##### ERROR ------------------------------------------------------------------------------------------
Please suggest an edit in the command to fix this.
Thank you