SomaticVarPipe

Repository to hold information on how to run GATK Mutect2 Somatic Variant discovery on Argon at UIowa

How to do Mutect2 calling

1. Create bam files from the reads and sort ./createbams.sh

2. Add missing Read Groups to the read headers ./add_RG.sh

3. Run Mutect2 in your tumor only mode ./tumorOnlyMode.sh

4. Create DataBase to be used in making the Panel of Normals ./createGenomicsDB.sh

5. Make Panel of Normals (PON) ./createPON.sh

6. 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