SystemSystem Posts: 226Administrator admin
edited July 2012 in Tool Bulletin

A new tool has been released!

Check out the documentation at BaseRecalibrator.


  • jlrfloresjlrflores Posts: 14Member

    The documentation says "This walker is designed to work as the first pass in a two-pass processing step..." How is the second pass run?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,682Administrator, GATK Dev admin

    The second step uses PrintReads. See this article for details:

    Geraldine Van der Auwera, PhD

  • seqseekseqseek Posts: 11Member
    edited October 2012

    Just to report a small bug here.
    The dbSNP vcf in hg19 bundle has header for both b37 and hg19. But the lengths for chrM are different.


    BaseRecalibrator will report error using this dbSNP as knownSites. Removing the b37 header solved the problem.

    Post edited by Geraldine_VdAuwera on
  • ebanksebanks Broad InstitutePosts: 689Member, Administrator, GATK Dev, Broadie, Moderator, DSDE Dev, GP admin

    Thanks for reporting this, but I just tested it and it doesn't generate any errors. Perhaps you are using the b37 reference and not hg19?

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

  • yunfeiyunfei Posts: 1Member

    I try to run BaseRecalibrator using the next command:
    java -jar ${gatk}/GenomeAnalysisTK.jar -T BaseRecalibrator -R ref.fa -I realigned.bam -o recal.table

    It said I must provide a VCF file containing known sites of genetic variation.
    why -knownSites cannot be skip? Where can I download this kind of VCF file.


  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,682Administrator, GATK Dev admin

    @yunfei, You cannot skip this parameter because the function of the tool depends on it. See the documentation for more details. We provide the necessary files for human analysis in our resource data bundle. See the FAQs for information on how to access the bundle.

    Geraldine Van der Auwera, PhD

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