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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Three questions about calling CNV in Germline.

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    Genevieve Brandt (she/her)

    Yes, the JointGermlineCNVSegmentation tool was released in 4.2.0.0. There are release notes available here: https://github.com/broadinstitute/gatk/releases/tag/4.2.0.0

    Here are some notes as it was being built as well: https://github.com/broadinstitute/gatk/pull/6554

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    Genevieve Brandt (she/her)

    Hi rq m,

    Here are the answers to your three questions, hope this helps!

    1. Yes, you should run these batches separately.
    2. Yes, you can change the ploidy in that file.
    3. Run GATK 4.2.

    Best,

    Genevieve

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    rq m

    Hi Genevieve Brandt.

    Thanks for your answer.
    I have understood question 1 and 2, but I still have doubts about question 3.
    I have used version 4.2. I called CNV according the tutorial (How to) Call common and rare germline copy number variants.

    In the end, I generated many VCF files. But, each VCF file contains only one sample CNV information. How can I get all samples CNV information in ONE VCF file, like calling SNP?

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    SkyWarrior

    There is a new tool called JointGermlineCNVSegmentation. There is no clear documentation available yet but you can try. I will be trying it in a few days. 

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    Archana Verma

    Hi, I have one confusion, how to change the ploidy of a chromosome to 2 from 3. 

    Is the example below is right?

    CONTIG_NAME     PLOIDY_PRIOR_0                            PLOIDY_PRIOR_1                                                  PLOIDY_PRIOR_2 PLOIDY_PRIOR_3
    I 0.01 0.98 0.01 0
    II 0.01 0.98 0.01 0
    III 0.01 0.98 0.01 0
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    Pamela Bretscher

    Hi Archana Verma,

    Yes, this should work. Setting the prior probability to 0 will remove that ploidy state and forbid the tool from assuming a ploidy of 3. There is additional information in the DetermineFermlineContigPloidy Tool Documentation. Please let me know if this answers your question.

    Kind regards,

    Pamela

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    Archana Verma

    Hi Pamela Bretscher,

    Thanks for your answer.
    I have understood the explanation.

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