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Empty output when using VariantsToVCF with a simple BED file

kevyinkevyin Member
edited September 2013 in Ask the GATK team

java -Xmx2g -jar /share/ClusterShare/software/contrib/gi/gatk/2.6-4-g3e5ff60/GenomeAnalysisTK-2.6-4-g3e5ff60/GenomeAnalysisTK.jar -R /share/ClusterShare/biodata/contrib/gi/gatk-resource-bundle/2.3/hg19/ucsc.hg19.fasta -T VariantsToVCF -o bedtovcf.vcf --variant:BED single.bed --dbsnp /share/ClusterShare/biodata/contrib/gi/gatk-resource-bundle/2.3/hg19/dbsnp_137.hg19.vcf -L chr1

single.bed

chr1 10153 10154 1

The output is empty

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Best Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MA admin
    Accepted Answer

    You could probably write a script to generate dummy VCF records from the BED intervals; you'd need to include a function to retrieve the ref sequence.

    Or you could make your life much, much easier and just call variants on your reference using the BED file as intervals list (see -L argument) in EMIT_ALL_SITES mode of the UnifiedGenotyper. That will produce a valid VCF that you can then edit to fit your needs.

Answers

  • kevyinkevyin Member

    @Geraldine_VdAuwera
    Hi there, thx for the reply.
    Is there any format I can use to make a set of custom locations and create a "skeleton" vcf from it?
    Cheers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Accepted Answer

    You could probably write a script to generate dummy VCF records from the BED intervals; you'd need to include a function to retrieve the ref sequence.

    Or you could make your life much, much easier and just call variants on your reference using the BED file as intervals list (see -L argument) in EMIT_ALL_SITES mode of the UnifiedGenotyper. That will produce a valid VCF that you can then edit to fit your needs.

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