I am using GATK VariantsTOVCF to convert .txt format to .vcf format and met the error. The commands I used are as follows,
$ java -jar GenomeAnalysisTK.jar -R genome.fa -T VariantsToVCF --variant:mm10 snp137.txt -o snp137.vcf
Here is the ERROR information, not quite understand what is it exact mean since I am new to use this software
ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.7-4-g6f46d11):
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](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:
See more at: http://gatkforums.broadinstitute.org/discussion/3392/variantstovcf#latest
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written
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Tonyzeng •
Thank you Vivek, I have made some modifications as follows.
$ java -jar GenomeAnalysisTK.jar -T VariantsToVCF -V:OLDDBSNP snp137.txt -R genome.fa -o snp137.vcf
Ashutoshmits and Vivek, thank you for your suggestion. I used the following commands. It works this time, however, the snp137.vcf file has the size as 0 when I checked it from Linux. It seems like I missed something there when I run VariantsToVCF. the 2 other other files have been generated as snp137.txt.idx and snp137.txt.idx.
$ java -jar GenomeAnalysisTK.jar -T VariantsToVCF -V:OLDDBSNP snp137.txt -R genome.fa -o snp137.vcf
I have the same problem. When I run the Variants to VCF converter command, it gives me back 3 files: snp138.txt.idx, snp138.vcf and snp138.vcf.idx. The problem is that the .vcf file has a size of 0. I used the same commands as Tonyzeng.
This is what I get back:
INFO 12:03:51,135 HelpFormatter - ---------------------------------------------------------------------------------
INFO 12:03:51,141 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.6-13-g91f02df, Compiled 2012/06/26 20:27:56
INFO 12:03:51,142 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 12:03:51,143 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 12:03:51,144 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 12:03:51,147 HelpFormatter - Program Args: -R /import1/genome/mm10/mm10.fa -T VariantsToVCF --variant:OLDDBSNP /data1/sowmya/mousedata/snp138.txt -o /data1/sowmya/mousedata/snp138.vcf
INFO 12:03:51,148 HelpFormatter - Date/Time: 2014/06/11 12:03:51
INFO 12:03:51,150 HelpFormatter - ---------------------------------------------------------------------------------
INFO 12:03:51,167 HelpFormatter - ---------------------------------------------------------------------------------
INFO 12:03:51,252 GenomeAnalysisEngine - Strictness is SILENT
INFO 12:03:51,764 RMDTrackBuilder - Creating Tribble index in memory for file /data1/sowmya/mousedata/snp138.txt
INFO 12:14:33,520 IndexDictionaryUtils - Track /data1/sowmya/mousedata/snp138.txt doesn't have a sequence dictionary built in, skipping dictionary validation
INFO 12:14:33,523 RMDTrackBuilder - Writing Tribble index to disk for file /data1/sowmya/mousedata/snp138.txt.idx
INFO 12:14:35,499 TraversalEngine - Total runtime 1.24 secs, 0.02 min, 0.00 hours
WARN 12:14:37,824 RestStorageService - Error Response: PUT '/GATK_Run_Reports/fj6NIgI0hZ0o7ihEDJFOD1RAOQQEff4t.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 325, Content-MD5: rTNushoF7Dpb0/NHwgPrEA==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: ad336eb21a05ec3a5bd3f347c203eb10, Date: Wed, 11 Jun 2014 16:14:36 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:H7fZOR6VqIYXsbW251c1tz0DCNY=, User-Agent: JetS3t/0.8.1 (Linux/3.5.0-49-generic; amd64; en; JVM 1.7.0_60), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: F8B340C9A87E6DA2, x-amz-id-2: k861aaq4Ion0f8kxLHVrRe/5VvlRoPh6RFSU06OwKriPLkfiortzOHJvKbor+kha, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Wed, 11 Jun 2014 16:14:37 GMT, Connection: close, Server: AmazonS3]
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It clearly says not to post it on GATK forum but you still pasted it which is not cool. As it says there is sth wrong with your input command. Can you paste the usage for VariantsToVCF feature of GATK.
Thank you for your reminding, ashutoshmits. there is no details for the usage of VariantsToVCF in GATK pakage but from the Broad institute website as http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_VariantsToVCF.html