Repository to hold information on how to run GATK Mutect2 Somatic Variant discovery on Argon at UIowa
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Create bam files from the reads and sort
./createbams.sh -
Add missing Read Groups to the read headers
./add_RG.sh -
Run Mutect2 in your tumor only mode
./tumorOnlyMode.sh -
Create DataBase to be used in making the Panel of Normals
./createGenomicsDB.sh -
Make Panel of Normals (PON)
./createPON.sh -
Call mutations by Mutect2
./mutect2_calling.sh
7-a. (Optional Branch-1) Convert VCF into tsv format that can be next used by pandas
vcf_to_tsv.sh
7-b. (Optional Branch-2) Convert VCF into MAF format that can be used for clustering
| FileName | Short Description |
|---|---|
| createbams.sh | takes input reads and outputs bam files |
| tumorOnlyMode.sh | Runs Mutect2 in a tumor-only mode |
| add_RG.sh | adds Read Groups with sample information to the reads headers |
| createGenomicsDB.sh | Create DataBase to be used in making the Panel of Normals |
| createPON.sh | For creating PON by using GenomicDB |
| mutect2_calling.sh | Mutect2 mutation calling script |
| vcf_to_tsv.sh | Convert VCF into tsv format |