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LiftoverVariants fails to update the header

nilshomernilshomer Boston, MAPosts: 11Member, Dev
edited May 2013 in Ask the GATK team

When running the LiftoverVariants command, the resulting VCF header has the old contig names (ex. b37 to hg19, chromosome one's name is still "1" rather than "chr1"). This only affects the header, while the variants themselves are successfully changed. I am running "2013.1-2.4.9-3-g512dc3e". The command I used is shown below:
<gatk> -R <human_g1k_v37>.fasta -T LiftoverVariants -V <in>.vcf -dict <hg19>.dict -o <out>.vcf -chain <b37tohg19>.chain

Thanks for your help!

Best Answer

  • ebanksebanks Broad InstitutePosts: 698Member, Administrator, Broadie, Moderator, Dev admin
    Answer ✓

    Hey Nils,

    LiftoverVariants is intended to be the first of 2 processing steps for the liftover; the second step is FilterLiftedVariants. In fact, LiftoverVariants is not guaranteed to produce a valid VCF file (which is alluded to in the documentation but I will go ahead and make it much more clear). If you run FilterLiftedVariants on the output of LiftoverVariants you'll see that the contig names in the header have all been correctly replaced.

    Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

Answers

  • ebanksebanks Broad InstitutePosts: 698Member, Administrator, Broadie, Moderator, Dev admin
    Answer ✓

    Hey Nils,

    LiftoverVariants is intended to be the first of 2 processing steps for the liftover; the second step is FilterLiftedVariants. In fact, LiftoverVariants is not guaranteed to produce a valid VCF file (which is alluded to in the documentation but I will go ahead and make it much more clear). If you run FilterLiftedVariants on the output of LiftoverVariants you'll see that the contig names in the header have all been correctly replaced.

    Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

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