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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

How do I call variants from somatic RNA data?

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    Genevieve Brandt (she/her)

    Hi Peiwen Li,

    I am going to move your post into our Community Discussions -> Special GATK Use Cases topic, as the Non-Human topic is for reporting bugs and issues with GATK.

    You can read more about our forum guidelines and the topics here: Forum Guidelines.

    Best,

    Genevieve

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    Genevieve Brandt (she/her)

    Hi Peiwen Li, it depends on if you are looking to find differences between your samples and a reference? Or, your samples to a normal + reference? You can read more about the distinction in this article: Somatic calling is NOT simply a difference between two callsets

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    Peiwen Li

    Hi Genevieve-Brandt-she-her,

    Thank you for your replies and I am sorry I posted my questions to the wrong place. 

    I am looking to find differences between my samples and a reference. And after reading the article you shared, I think my situation is more fitted into the HaplotypeCaller's algorithm?

    Thank you,

    Peiwen

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    Genevieve Brandt (she/her)

    I think so! Glad it helped to clarify!

    Have a good weekend,

    Genevieve

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    Peiwen Li

    Hi Genevieve-Brandt-she-her,

    I have a confusion on the "RNAseq short variant discovery (SNPs + Indels)" GATK Best practices workflow. It suggests to use per-sample variant calling for RNAseq data. What does that mean exactly? If I have multiple BAM inputs, should I run HaplotypeCaller for each of them one at a time, and get multiple VCF outputs? Then how can I get ONE single concordant multi-sample VCF for all VCF outputs?

    Thank you so much and I hope you have a great weekend!

    Peiwen 

     

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    Genevieve Brandt (she/her)

    Hi Peiwen,

    Joint calling is not supported yet for this method. With this best practices pipeline you will get multiple VCF outputs if you have multiple BAM inputs.

    Genevieve

     

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