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RNA-seq variant calling for somatic

barbarianbarbarian JapanMember
edited February 2017 in Ask the GATK team

I want to find best practice to do variant calling from this page : https://software.broadinstitute.org/gatk/best-practices/
I have exome-seq and RNA-seq data and I think because the sample is from human cancer, the workflow I need to follow is somatic. I don't see any best practice that use RNA-seq for somatic cell. Any suggestion which best practice I should follow and which data, RNA-seq or exome-seq I should use? Thank you.

Answers

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @barbarian,

    Please checkout the workflows in FireCloud. Perhaps they have some analyses that integrate somatic RNA-Seq data. The FireCloud workflows are from the Broad Cancer Genome Analysis group and should represent approaches from TCGA (The Cancer Genome Atlas) studies, which you can learn more about from the FireBrowse website.

    In terms of GATK Best Practices, our RNA workflows work well for some users and are geared toward variant calling. It is up to you to decide how you want to preprocess your data. For differential expression, you should look elsewhere for recommendations.

  • barbarianbarbarian JapanMember

    @shlee said:
    Hi @barbarian,

    Please checkout the workflows in FireCloud. Perhaps they have some analyses that integrate somatic RNA-Seq data. The FireCloud workflows are from the Broad Cancer Genome Analysis group and should represent approaches from TCGA (The Cancer Genome Atlas) studies, which you can learn more about from the FireBrowse website.

    In terms of GATK Best Practices, our RNA workflows work well for some users and are geared toward variant calling. It is up to you to decide how you want to preprocess your data. For differential expression, you should look elsewhere for recommendations.

    I want to do variant calling but I have read somewhere before in GATK, the exome seq coverage is small compare to RNA-seq so data from exome-seq is not good for variant calling. That's why I tried to do variant calling using RNA-seq. So, is using exome-seq good enough now? I have done variant calling before but it was 2 years ago. So, maybe the new software is getting better.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @barbarian

    Hi,

    What exactly is your end goal?

    Have a look at this thread and this thread for RNA-seq data help.

    As for exome data, have a look at the Best Practices page.

    -Sheila

  • barbarianbarbarian JapanMember

    @Sheila said:
    @barbarian

    Hi,

    What exactly is your end goal?

    Have a look at this thread and this thread for RNA-seq data help.

    As for exome data, have a look at the Best Practices page.

    -Sheila

    My end goal is to get variation. I have tried samtools+bcftools to call variation. The output of bcftools is vcf file and that is what I want. It is pretty basic actually. I just want to ask whether BAM which come from RNA-seq experiments can be used for GATK variant calling. I ask this question because there are no best practice mentioned for RNA-seq. So, I want to confirm whether RNA-seq data can be used too for variant calling. I remember around 2 years ago, I used RNA-seq data for one of GATK tools and the result is quite good. I just forget which best practice/workflow I used.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @barbarian
    Hi,

    Okay. Then, I think you should find the two threads I linked to in the previous answer helpful. Also, have a look here for RNA-seq Best Practices. Note, you will need to adapt the workflow for cancer data.

    -Sheila

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