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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

UMI-tools dedup, index BAM file and run samtools stats, flagstat and idxstats

umidedupindexbamsamcram

Included in: nascentrnaseq

Calculate contamination of the X-chromosome with ANGSD

angsdbamcontaminationdocounts

Picard MarkDuplicates, index BAM file and run samtools stats, flagstat and idxstats

markduplicatesbamsamcram

Included in: atacseqcircdnarnadnavar +2 more pipelines

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

Included in: rnadnavar

Subworkflow to run multiple commands in the RSeqC package

rnaseqexperimentinferexperimentbamstatinnerdistancejunctionannotationjunctionsaturationreaddistributionreadduplicationtin

Included in: callingcardsrnaseq

Sort SAM/BAM/CRAM file

sortbamsamcram

Included in: atacseqcircrnacutandrun +7 more pipelines

Split the reads in the input bam by specified genomic region.

splitbamsamcramindex

Produces comprehensive statistics from SAM/BAM/CRAM file

statisticscountsbamsamcram

Included in: atacseqcallingcardscircdna +9 more pipelines

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

Included in: rnadnavar