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TMB

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  • Refseq accession number and version number in Funcotator

    Answered

    I used Funcotator to annotate my VCF (somatic variant calling) and worked great.  Now I have to find the correct RefSeq number and version number of the reference sequence used to annotate variants...

  • Funcotator gnomAD MAF columns

    Answered

    Hi I used Funcotator to annotate VCF (somatic variant calling).  I am tying to filter out variants based on MAF and would like to use a female population (inclusive for all ancestries).  I have use...

  • Mutect2 failing to produce F1R2.tar.gz files on TCGA bam (tumor-normal pairs)

    Answered

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.9.0b) Exact command used:   gatk --java-options "-Xmx6G" Mutect2 -R $REF -I ${BAM_DIR}/${BN}_NORMAL_DNA.fixed.bam -I...

  • Germline false positives in Mutect2

    If not an error, choose a category for your question(REQUIRED):c) Why do I see a large number of false positive (especially germlines) after calling somatic variants by Mutect2?  d) Where do I find...

  • Funcotator: VCF output

    I am new to gatk as well as the forum. According to the Funcotator tutorial online (excerpt below), the recommendation is using both of two gnomAD sources (exome and whole genome). It’s not clear i...