M Carta
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Mutect2 forced calling via --alleles does not always generate an output
I am attempting to force Mutect2 to call a particular variant of interest, given in variant.vcf.gz, using the following command: gatk Mutect2 \-R "hg38.fa" \--alleles "variant.vcf.gz" \-L "variant....
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Does IGV perform filtering when displaying reads?
I have noticed that the read counts displayed in IGV are slightly lower than those in the AD field in the respective VCF files. Is it possible that IGV does not display certain reads (perhaps poor ...
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Is there a GATK tool for quantifying a particular base?
Apologies if this is a naive question, but I'm quite new to bioinformatics.I'm working with targeted Illumina sequencing data generated with DNA from diseased and healthy tissue (this is an age-rel...
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Mutect2 Unable to trim uncertain bases without flow order information
Hi everyone. I'm trying to run Mutect2 on some Illumina sequencing files that were processed as follows (GATK best practices): trimmed with Trimmomatic, mapping with Minimal2, converted to BAM with...