In your guild, it use human_g1k_v37_decoy.fasta and 1000G_phase3_v4_20130502.sites.vcf ...
Can i use hg19 reference instead of human_g1k_v37_decoy.fasta ?

Can i skip VQSR step ?

Best Answers


  • I have 4 exome samples.
    mother, father, child1(normal), child2(patient)

    In this case,
    Do i run Genotypegvcf multiple calling and Genotype refinement at once about 4 samples or run twice each case( mother, father, child1 // mother, father, child2 )

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    You should run GenotypeGVCFs on all the samples GVCFs together.

    After that, you can either skip VQSR, or add exomes from the 1000G project in order to collate enough data to run VQSR, as described in our documentation.

  • ok, i got it..
    but after that..
    When i run Genotyoe refinement,

    can i run about 4 samples at once or twice each case( mother, father, child1 // mother, father, child2 ) ?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    You will have to run it twice, as the workflow tools accept trio pedigrees.


  • sorry, my english is bad.

    I used the following...
    step 1. haplotypecaller in GVCF mode each sample.(father,mother,child)
    step 2. GenotypeGVCF from trio sample together at once.
    step 3. Genotype refinement
    (CalculateGenpytePosteriors -> VariantFiltration -> VariantAnnotator )
    step 4. i got hiConf and loConf denovo mutation ..

    My question is that before step 3, should i run pass PhasebyTransmission process?
    I read the different abount phasing information of haploytpeCaller and phasebytransmission .

    in addition,
    I think in this case, phasing information from family relation is needed. but haplotypecaller's phase information is from physical phasing information from the same active region window.
    I wonder why doesn't exist that in your genotype refinement example method ?

    am i wrong?

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