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Picard 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
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CatVariants or CombineVariants

If I want to merge different VCF files, which I used -L argument for calling variants against to different chromosomes individually with the same list of samples by HaplotypeCaller. I mean the sample are the same, I just used -L to call variants chromosome by chromosome separately. I suppose whether catVariants or CombineVariant will give me the same results, right ?


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Yes, they will give you the same results; only the headers will be slightly different because CatVariant will just use the header of the first VCF file, while CombineVariants will generate a new header. CatVariants is faster.

  • jacobhsujacobhsu Hong KongMember

    Thanks for quick reply. Here is the original command I tried

    ${java7} -Xmx2g -jar $GATK/GenomeAnalysisTK.jar \
    -R $reference_genome \
    -T CombineVariants \
    --variant $inputdir/chr01.vcf \
    --variant $inputdir/chr02.vcf \
    --variant $inputdir/chr03.vcf \
    --variant $inputdir/chr04.vcf \
    -o $vcf_output \
    -nt 8 \
    -genotypeMergeOptions UNIQUIFY

    Will that be different than this ?

    ${java7} -cp $GATK/GenomeAnalysisTK.jar \
    -R $reference_genome \
    -V $inputdir/chr01.vcf \
    -V $inputdir/chr02.vcf \
    -V $inputdir/chr03.vcf \
    -V $inputdir/chr04.vcf \
    -out $vcf_output \

    As you mentioned it, the CombineVariants will generate another header and the size is larger than CatVariants very much, but the content is the same. Could you please explain more ?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    The results, in terms of how variant records are combined, should be essentially the same if the files you are merging involve all the same samples, just different chromosomes. What differences are you observing exactly? Can you maybe post the headers?

  • mglclinicalmglclinical USAMember

    Hi @Geraldine_VdAuwera ,

    I am usig GATK 3.5

    I am doing per chromosome HaplotypeCaller (in GVCF mode) calls with -L argument, which is similar to what @jacobhsu is doing.

    I know that CatVariants can be used to concatenate .vcf files for a given sample.

    I would like to confirm that CatVariants can also be used to concatenate .g.vcf files ?

    I am asking this question because in the CatVariants documentation here, there is no mention of .g.vcf files


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi @mglclinical, yes CatVariants works on GVCFs as they are valid VCFs.

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