Perform variant calling on a set of normal samples using mutect2 panel of normals mode. Group them into a genomicsdbworkspace using genomicsdbimport, then use this to create a panel of normals using createsomaticpanelofnormals.
gatk4mutect2genomicsdbimportcreatesomaticpanelofnormalsvariant_callinggenomicsdb_workspacepanel_of_normals
Calculate contamination of the X-chromosome with ANGSD
angsdbamcontaminationdocounts
Samtools markduplicate SAM/BAM/CRAM file
markdupbamsamcram
Take a set of bam files and run NGSCheckMate to determine whether samples match with each other, using a set of SNPs.
ngscheckmateqcbamsnp
Produces comprehensive statistics from BAM file
statisticscountshs_metricswgs_metricsbamsamcram
Subworkflow to run multiple commands in the RSeqC package
rnaseqexperimentinferexperimentbamstatinnerdistancejunctionannotationjunctionsaturationreaddistributionreadduplicationtin
Split the reads in the input bam by specified genomic region.
splitbamsamcramindex
Produces comprehensive statistics from SAM/BAM/CRAM file
statisticscountsbamsamcram
Perform variant calling on a paired tumor normal set of samples using mutect2 tumor normal mode. f1r2 output of mutect2 is run through learnreadorientationmodel to get the artifact priors. Run the input bam files through getpileupsummarries and then calculatecontamination to get the contamination and segmentation tables. Filter the mutect2 output vcf using filtermutectcalls, artifact priors and the contamination & segmentation tables for additional filtering.
gatk4mutect2learnreadorientationmodelgetpileupsummariescalculatecontaminationfiltermutectcallsvariant_callingtumor_onlyfiltered_vcf