Variant calling design

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  • smk_84smk_84 Member

    Hi all,

    I have 4 cancer cell lines exomes that I am trying to run with GATK. They are all breast cancer cell line subtypes. I have called the variants on them individually. I was wondering if it is more advisable to call the variants together or it is better to call variants individually. Along the same lines should I do joint genotyping on them.


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @smk_84

    Here is a doc that has information on steps to call somatic variants. Mutect2 is the tool used to call these variants and more info on that can be found here.

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