To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

trio pipeline

Dear friends
I am analyzing a trio
I have followed the pipeline described in van der Auwera et al. 2013
on each person individually up to HaplotypeCaller and VariantRecalibrator

is there a pipeline I can follow to put together the data and recognize disease variants in the affected child (de novo or inherited?)
thank you vittoria

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @vittoria
    Hi Vittoria,

    You may find the Genotype Refinement Workflow useful. You can find more information in the presentations section and Methods and Algorithms section.

    -Sheila

  • thank you sheila

    I understand that the first step is running

    java -jar GenomeAnalysisToolkit.jar -R human_g1k_v37_decoy.fasta -T CalculateGenotypePosteriors --supporting 1000G_phase3_v4_20130502.sites.vcf -ped trio.ped -V recalibratedVariants.vcf -o recalibratedVariants.postCGP.vcf

    I understand that recalibratedVariants.vcf combines the variants of the father, the mother and the child
    i.e. triorecalibratedVariants.vcf
    but
    I have produced the recalibratedVariants.vcf for father, mother and child separately

    how do I put them together
    fatherrecalibratedVariants.vcf, motherrecalibratedVariants.vcf childrecalibratedVariants.vcf -->
    triorecalibratedVariants.vcf

    moreover can I find .ped file I can modify with my data?

    thank you

    vittoria

  • Dear Sheila, thank you

    I understand that I have to run something like

    java -jar GenomeAnalysisToolkit.jar -R human_g1k_v37_decoy.fasta -T CalculateGenotypePosteriors --supporting 1000G_phase3_v4_20130502.sites.vcf -ped trio.ped -V recalibratedVariants.vcf -o recalibratedVariants.postCGP.vcf

    I assume that recalibratedVariants.vcf contains variants of the father, of the mother and of the kid
    I have 3 recalibrated vcf files one for the father, one for the mother and one for the kid
    how do I put together the files?
    second:
    I do I get an example of trio.ped? I would like to modify one

    thank you very much

    vittoria

    Issue · Github
    by shlee

    Issue Number
    2305
    State
    closed
    Last Updated
    Assignee
    Array
    Closed By
    chandrans
  • shleeshlee CambridgeMember, Broadie, Moderator
    edited July 2017

    Hi @vittoria,

    Sheila is away at a workshop and can followup on your questions when she is back in Boston next week.

    In the meanwhile, this thread and this thread may be of interest.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @vittoria
    Hi Vittoria,

    For the trio VCF, we recommend running the GVCF workflow. However, if you must, you can simply use CombineVariants to combine the three VCFs into one VCF.

    For creating the ped file, have a look here.

    -Sheila

  • Dear friends, I generated a joint vcf file for a trio but I have problems visualizing it with igv. where can I find a sample file to see how a correct file should appear in igv? where is the information in each variant concerning the identity (son, father or mather)? I do not understand how I see whether a mutation is present in the sono but not in the parents and so on
    thank you maria vittoria

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @vittoria
    Hi Maria,

    I think you will find the Variant Discovery tutorial here helpful.

    -Sheila

  • I have a trio whole exome data set, based on the VQSR documentation it seems that 3 samples is too few to run with VQSR. Is that correct? What is the best option in this?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @artitandon
    Hi,

    Yes, 3 exome samples are not enough for VQSR. We recommend using at least 30 exome samples. You can try hard filtering.

    -Sheila

Sign In or Register to comment.