Software for Clinical Health Omics Onocolgy Laboratories

School is a collection of genomics analysis workflows that are used for detecting single nucleotide variants (SNVs), insertions/deletions (indels), copy number variants (CNVs) and translocations from RNA and DNA sequencing. These workflows have been validated in a CLIA laboratory at UTSW

Nextflow Workflows

SlideRule: DNA Workflow

using Module nextflow/20.01.0

nextflow -C ${nfhome}nextflow.config run -w $workdir ${nfhome}/dna.nf --input fastq --output analysis --design design.txt --seqrunid $seqrunid --pon $mutectpon --capture $capturebed --capturedir $cnvkitref --version $gittag --genome $dna_ref_path --markdups $markdup_method

seqrunid = Illumina Run ID, used to distrinquished repetative runs mutectpon = capturebed = Hyb Gene Capture Kit Bed File markdup_methd = picard, samtools, fgbio_umi, picard_umi and none

DNA Design File

SampleID	TumorID	NormalID	FamilyID	FqR1	FqR2
Sample1	Sample1	Sample2	Fam1	Sample1.R1.fastq.gz	Sample1.R2.fastq.gz
Sample2	Sample1	Sample2	Fam1	Sample2.R1.fastq.gz	Sample2.R2.fastq.gz
Sample3	Sample3	Sample4	Fam2	Sample3.R1.fastq.gz	Sample3.R2.fastq.gz
Sample4	Sample3	Sample4	Fam2	Sample4.R1.fastq.gz	Sample4.R2.fastq.gz

markdup_methd = picard, samtools, fgbio_umi, picard_umi and none

Abbacus: RNASeq Workflow

nextflow -C nextflow.config run -w workdir rnaseq.nf --design design.txt --input dir_with_fastqs --output results_output --markdups markdup_method