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avrajit

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Latest activity by avrajit
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    avrajit commented,

    1. Community
    2. Somatic
    3. Multi sample somatic calling Mutect2

    Hi Gokalp Thanks for your response. 

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    avrajit created a post,

    Multi sample somatic calling Mutect2

    1. Community
    2. Somatic

    REQUIRED for all errors and issues: a) GATK version used:4.5.0b) Exact command used: c) Entire program log: I like to know how  I do variant calling for multiple pairs of  Normal- tumor samples wi...

    • avrajit
    • 2 followers
    • 2 comments
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    avrajit commented,

    1. Community
    2. General Discussion
    3. Somatic Mutation and PON creation

    Hi Pamela, Thanks for your response. I also thought the same. Just looking for a confirmation. Thanks a lot.

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    avrajit created a post,

    Somatic Mutation and PON creation

    Answered
    1. Community
    2. General Discussion

    To identify somatic mutation Mutect2  need 3 items 1. matched tumor-normal sample 2. a germline  variant of population data e.g. "somatic-hg38_small_exac_common_3.hg38.vcf" 3. And a Panel of Normal...

    • avrajit
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    avrajit commented,

    1. Community
    2. Somatic
    3. Mutect2 PON VCF

    I found GATK references follow ucsc hg38. Coding. Using ucsc hg38 can solve the problem. I did the same. Thanks

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    avrajit created a post,

    Mutect2 PON VCF

    1. Community
    2. Somatic

    a) GATK version used: 4-4.1.4.1-0b) Exact command used: gatk Mutect2 -R /home/refererence/GRCh38PicardIDX/GRCh38.p12_genomic.fa -I /home/NewExomeBC2020/sorted_RBRN02_Dedup.bam -tumor RBRN02 --germl...

    • avrajit
    • 3 followers
    • 3 comments
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