Error When Convert Mouse Snp137.Txt To .Vcf Format

Question

[Tonyzeng]

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

[Ashutosh Pandey]

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.

[Tonyzeng]

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

Answer 1

[Vivek]

You need to sepcify the input file format to GATK that you wish to convert to VCF. Also the file needs to be coordinate sorted.

java GenomeAnalysisTK.jar -T VariantsToVCF -V:OLDDBSNP snp137.txt.sorted -R UCSC_Mouse_MM10.fasta -o snp137.vcf

[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

Answer 2

[Tonyzeng]

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

[sowmya.kuruganti]

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]