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GATK 3.3 Bad input: VCFHeaderLine: ID cannot contain angle brackets

ravichavravichav United StatesMember
edited November 2015 in Ask the GATK team

I am trying to run Variantfiltration on a VCF in a VCF4.1 format but end up getting this error. I removed the angle brackets from the VCF too and still running into this error. Thanks in advance!

java -Xmx12G -jar /programs/GATK-3.3-0/GenomeAnalysisTK.jar -T VariantFiltration -R hs37d5.fa -V temp.vcf --filterExpression "QD < 20 || FS < 20 || MQRankSum < -3 || MqRankSum > 3 || InbreedingCoeff < -0.2 || InbreedingCoeff > 0.5" --filterName "QD < 20 || FS < 20 || MQRankSum < -3 || MqRankSum > 3 || InbreedingCoeff < -0.2 || InbreedingCoeff > 0.5" -o filtered_variants.vcf

INFO 16:21:24,770 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:21:24,770 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:21:24,871 GenomeAnalysisEngine - Strictness is SILENT
INFO 16:21:25,015 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 16:21:25,268 GenomeAnalysisEngine - Preparing for traversal
INFO 16:21:25,286 GenomeAnalysisEngine - Done preparing for traversal
INFO 16:21:25,287 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 16:21:25,288 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 16:21:30,825 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.3-0-g37228af):
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 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 Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR MESSAGE: Bad input: VCFHeaderLine: ID cannot contain angle brackets
ERROR ------------------------------------------------------------------------------------------

Best Answer


  • pdexheimerpdexheimer Member ✭✭✭✭

    The angle brackets are in your filter name. The text given with the --filterName parameter become the ID for that filter, and so can't contain < or > signs.

    Also, you probably don't want all of the filters in a single statement, because it won't behave the way you expect for variants with missing annotations. Somewhere that I can't look up right now, there's a document on using hard filters

  • ravichavravichav United StatesMember

    Cool ! Thanks. Everytime there is a ID followed by a value then everything below that value will be removed by default? How may I specify a range in this filter or greater than a value?

  • ravichavravichav United StatesMember

    Got it! Thanks again

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