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Leore Nehemie Bensabath

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Latest activity by Leore Nehemie Bensabath
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    Leore Nehemie Bensabath created a post,

    Mutect2: NuMTs filtering on RNA-seq

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    Hi GATK Team,  I am using Mutect2 in mitochondrial mode on rat RNA-seq data (I don't have WGS data available).  It is not super clear to me if filtering NuMTs with the flag --autosomale-coverage of...

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    Leore Nehemie Bensabath commented,

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    Okay I understand. Thanks a lot, this is very helpful ! 

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    Leore Nehemie Bensabath commented,

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    David Benjamin thanks for your answer !   I am not sure if we are talking about the same kind of dosage, I am pretty new to the field. The genotype dosage I had in mind is the one defined as :  DS ...

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    Leore Nehemie Bensabath commented,

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    Thanks a lot ! 

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    Leore Nehemie Bensabath created a post,

    Dosages with Mutect2

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    a) GATK version used : gatk-4.1.3.0b) Exact GATK commands used : gatk Mutect2 -R ref.fa -L chrM --mitochondria-mode -I input.bam -O output.vcf gatk FilterMutectCalls -R ref.fa -autosomal-coverage 1...

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