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  • GATK test data for Mutect?

    1. Community
    2. New User Advice

    Am I correct that there exists no tumor-normal pairs of bams for testing Mutect at the GATK Test Data repository, or am I just not finding the data? (https://s3.amazonaws.com/gatk-test-data/gatk-te...

    • registered_user
    • 2 followers
    • 1 comment
    • 0 votes

  • DRAGMAP and Mutect?

    Answered
    1. Community
    2. General Discussion

    I was wondering if the open source DRAGMAP is currently compatible with Mutect? Is it possible to skip the BQSR step if using DRAGMAP instead of bwa-mem in PON creation and somatic variant calling ...

    • registered_user
    • Edited
    • 3 followers
    • 3 comments
    • 0 votes

  • ApplyBQSR wastes too much disk space

    1. Community
    2. General Discussion

    I have made the mistake of using the default compression level for ApplyBQSR and now I have terabytes of wasted space in my project bam files. The recalibrated files take up twice the disk space in...

    • registered_user
    • Edited
    • 3 followers
    • 4 comments
    • 0 votes

  • LeftAlignAndTrimVariants removes header tags

    1. Community
    2. Somatic

    I noticed that LeftAlignAndTrimVariants (GATK 4.1.8.1) keeps only the first entry of normal- and tumor sample header tags in VCF files. This is unexpected and unwanted behavior. Trimming should not...

    • registered_user
    • 2 followers
    • 1 comment
    • 0 votes

  • Mutect2 --alleles param GATK_4.1.7.0

    1. Community
    2. Somatic

    What's going on with the --alleles param for Mutect2? It will not accept a .vcf, .vcf.gz, .list or .intervals file (<chr>:<coordinate>). I have an index for the .vcf.gz file, .vcf.gz.tbi. I am gett...

    • registered_user
    • Edited
    • 2 followers
    • 2 comments
    • 0 votes

  • SelectVariants by genotype

    1. Community
    2. General Discussion

    I am trying to separate samples to individual VCF files from a multisample VCF file. What is the correct way to remove rows that are not present in the sample in the resulting VCF with SelectVarian...

    • registered_user
    • 4 followers
    • 8 comments
    • 0 votes

  • Increased number of false positives in Mutect2 GATK 4.1.7.0

    1. Community
    2. Somatic

    We are running Mutect2 on WGS prostate cancer samples. We analyzed our tumor-normal pairs previously with GATK 4.1.3.0 and validated the results against deep sequencing panel results (500-700x). We...

    • registered_user
    • Edited
    • 7 followers
    • 15 comments
    • 0 votes