This is a placeholder for a document in progress.
Articles in this section
- (How to) Run germline single sample short variant discovery in DRAGEN mode
- (How to) Generate an unmapped BAM from FASTQ or aligned BAM
- (Notebook) Intro to using Mutect2 for somatic data
- (How to) Install all software packages required to follow the GATK Best Practices
- (How to) Map and clean up short read sequence data efficiently
- (How to) Map reads to a reference with alternate contigs like GRCH38
- (How to) Fix a badly formatted BAM
- (Notebook) Concordance of NA19017 chr20 gCNV calls
- (How to part II) Sensitively detect copy ratio alterations and allelic segments
- (How to) Run GATK in a Docker container
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