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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

GenotypeGVCFs

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    Anthony Dias-Ciarla

    Hi Yumi Hashi,

    Thank you for writing to the GATK forum. I hope that we can help you sort this out.

    So when looking at your command line history, your second command seems inconsistent with the first command. When you ran the VcfToIntervalList command, it generated the interval file to the current directory, which is the parent of bwa_bam. In the GenomicsDBImport command, you specified the directory location as one step below the interval list you had just created with the first command.

    Try rerunning with the corrected commands and see if that works. If not, please let me know, and we can investigate further.

    Original:

    $gatk VcfToIntervalList 
     I=bwa_bam/gvcf/sample1_markdup.addRG.g.vcf 
     O=sample.interval_list

    $gatk GenomicsDBImport \
      --genomicsdb-workspace-path bwa_bam/GenomicDB \
      --intervals bwa_bam/sample.interval_list \
       --sample-name-map bwa_bam/gvcf_sample_name.txt


    Corrected:

    $gatk VcfToIntervalList \
     I=bwa_bam/gvcf/sample1_markdup.addRG.g.vcf \
     O=bwa_bam/sample.interval_list

    $gatk GenomicsDBImport \
      --genomicsdb-workspace-path bwa_bam/GenomicDB \
      --intervals bwa_bam/sample.interval_list \
       --sample-name-map bwa_bam/gvcf_sample_name.txt

    Best,
    Anthony

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