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GATK realigner

peijiapeijia taiwanMember

Hi,

I used the below command
"java -Xmx2g -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R ref.fa -I lib_sorted.bam -o lib.intervals -nt INT"
to run my data, but the program stoped when running "INFO 11:29:09,811 GenomeAnalysisEngine - Strictness is SILENT".

Can anyone tell me how to solve the problem? Thanks.

Answers

  • peijiapeijia taiwanMember

    Hi,

    I run rhino data according to the workflows ( http://www.htslib.org/workflow/ ).
    I use the below command
    "java -Xmx2g -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R ref.fa -I lib_sorted.bam -o lib.intervals -nt INT"
    to run the data, but the program stop when running the step ( INFO 11:29:09,811 GenomeAnalysisEngine - Strictness is SILENT ).
    But, I don't have the trouble when running spoonbill data.
    Can anyone tell me how to solve the problem?
    Thanks.

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @peijia
    Hi,

    Where are you getting the data from? And, are you getting FASTQ files and aligning those to a reference? Or, are you getting straight BAM files from some database?

    Thanks,
    Sheila

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