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Base recalibration: seeking help

Sir,
I was trying to recalibration_report.grp file using the following command:
java -Xmx16g -jar /Users/ZILLURRAHMAN/Desktop/PhD/GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -I Naushon.sorted.bam -R strain_naushan.fasta --knownSites Naushon.sorted.vcf -o recalibration_report.grp

But it gave me the following error report:

ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file 'Naushon.sorted.vcf' 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)

What should I do now?

Answers

  • zillurbmb51zillurbmb51 USAMember

    I have faced another problem:

    ERROR MESSAGE: SAM/BAM/CRAM file Naushon.bam is malformed: SAM file doesn't have any read groups defined in the header. The GATK no longer supports SAM files without read groups
    ERROR ------------------------------------------------------------------------------------------

    [zil[email protected] Naushan]$

  • zillurbmb51zillurbmb51 USAMember

    Hi,
    I was trying to use picard using the following lines. But it is always showing me unrecognised option.
    MacBook-Pro:Strain_Naushon ZILLURRAHMAN$ java -Xmx16g -jar /Users/ZILLURRAHMAN/Desktop/PhD/GATK/picard-tools-1.119/AddOrReplaceReadGroups.jar I=Naushon.sorted.bam O=Naushon.picard.bam \ PL=illumina ID=$RANDOM SM=mysample
    ERROR: Unrecognized option: PL

    java -Xmx16g -jar /Users/ZILLURRAHMAN/Desktop/PhD/GATK/picard-tools-1.119/AddOrReplaceReadGroups.jar I=Naushon.sorted.bam O=Naushon.picard.bam \ RGPL=illumina RGID=$RANDOM RGSM=mysample
    ERROR: Unrecognized option: RGPL

    MacBook-Pro:Strain_Naushon ZILLURRAHMAN$ java -Xmx16g -jar /Users/ZILLURRAHMAN/Desktop/PhD/GATK/picard-tools-1.119/AddOrReplaceReadGroups.jar I=Naushon.sorted.bam O=Naushon.picard.bam \ CREATE_INDEX=true \ RGPL=illumina RGID=$RANDOM RGSM=mysample
    ERROR: Unrecognized option: CREATE_INDEX

    Anyone help me.

  • SheilaSheila Broad InstituteMember, Broadie admin

    @zillurbmb51
    Hi,

    Can you tell me what version of GATK you are using? I think you need to upgrade to the latest version. https://www.broadinstitute.org/gatk/download/

    You also need to upgrade to the latest Picard release. The version you are using does not support the same arguments in the documentation. https://github.com/broadinstitute/picard/releases/tag/1.137

    -Sheila

  • zillurbmb51zillurbmb51 USAMember

    Thank you very much for your kind reply. My GATK is 3.4.0 and Picard is 1.119.

  • zillurbmb51zillurbmb51 USAMember

    picard 1.119 gave me many files(after unzip) but picard 1.137 gave me only four files after unzip. (htsjdk-1.137.jar
    libIntelDeflater.so
    picard-lib.jar
    picard.jar)

    Is it ok or I am doing anything wrong

  • KurtKurt Member ✭✭✭

    version 1.119 was the last version where every picard program had its own jar file. every release after this is where each program is called through picard.jar; e.g.

    java -jar picard.jar AddOrReplaceReadGroups

    version 1.119 and earlier would of been.

    java -jar AddOrReplaceReadGroups.jar

    ...as an aside, this made me think that I kind of miss getting the picard release notes from the samtools forum emails automatically....

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