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Noam Rudberg

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Latest activity by Noam Rudberg
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    Noam Rudberg created a post,

    VCF input example

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    Hi, I'm using gatk 4.2.6.1 to create a MAF file from vcf of variants. My problem is that many fields in the output MAF file are empty (such as - t_ref_count, t_alt_count, tumor_sample_barcode..). I...

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    Noam Rudberg commented,

    1. Community
    2. Germline
    3. Funcotator - all IGR classification

    Genevieve, thanks a lot! Adding the --force-b37-to-hg19-reference-contig-conversion flag worked.

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    Noam Rudberg commented,

    1. Community
    2. Germline
    3. Funcotator - all IGR classification

    Thanks! On the LiftOver page, there's a "b37tohg38.chain" chain file while there's no mention of b37 on the chain file download page. So I have two questions: 1. Do you know another source of chain...

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    Noam Rudberg commented,

    1. Community
    2. Germline
    3. Funcotator - all IGR classification

    Hi Genevieve-Brandt-she-her, new_vars.vcf is just a subset of the full VCF file I use to try Funcotator with, to save me some time until it works well :) Anyway, here's what you asked for: 16:54:29...

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    Noam Rudberg commented,

    1. Community
    2. Germline
    3. Funcotator - all IGR classification

    Hi Genevieve, Thanks for your response. I'm not sure I fully understand what your meaning is by looking into the VCF file. I used the ValidateVariants tool this way: gatk ValidateVariants -R Homo_s...

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    Noam Rudberg created a post,

    Funcotator - all IGR classification

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    1. Community
    2. Germline

    Hi, I saw this post but wasn't sure it's the same problem.I'm using gatk 4.2.6.1 using this command: gatk Funcotator --variant new_vars.vcf --reference Homo_sapiens_assembly19.fasta --ref-version h...

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