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  • ApplyBQSR wastes too much disk space

    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...

  • LeftAlignAndTrimVariants removes header tags

    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...

  • Mutect2 --alleles param GATK_4.1.7.0

    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...

  • SelectVariants by genotype

    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...

  • Increased number of false positives in Mutect2 GATK 4.1.7.0

    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...