dnanexus_applets

Trim Galore

trim_galore

Trim Galore: Trims poor quality sequence from read

Uses

• docker.io/goalconsortium/trim_galore:0.5.40
  • trim_galore_v0.4.1
  • cutadapt==1.9.1
• SCHOOL

Input

• Fastq Files (PE):
  • fq1
  • fq2
• Output Prefix Name

Output

• Fastq Files (PE):
  • fq1
  • fq2

DNA Alignment (dalign)

• BWA against the Human Genome
• BWA against the Viral Genom

Uses

• [docker.io/goalconsortium/alignment:0.5.40]((https://hub.docker.com/repository/docker/goalconsortium/alignment/general)
  • bwa 0.7.17
  • fgbio 1.1.0
  • picard 2.21.7
• SCHOOL

Input

• Fastq Files (PE):
  • fq1
  • fq2
• Human Ref: BWA Index Files for the Human Genome
• Virus Ref: BWA Index Files for the Virus Genome (optional)
• ReadGroup/SampleName

Output

• Sorted Human Ref BAM, BAI
• Viral alignment stats (optional)

ABRA2

abra2

Uses

• docker.io/goalconsortium/abra2:0.5.40
  • ABRA 2.20
  • samtools 1.10

Input

• Tumor BAM File
• Normal BAM File
• Reference Tar Gz file with genome.fa
• Panel Tar Gz with Target Panel Bed
• ReadGroup/SampleName

Output

• ABRA2 Tumor BAM
• ABRA2 Normal BAM
• ABRA2 Tumor BAM BAI
• ABRA2 Normal BAM BAI

DNA QC Stats

dna_bamqc

fastqc, coveragebed, samtools flagstat, picard EstimateLibraryComplexity

Uses

• Docker Container goalconsortium/vcfannot
• SCHOOL

Input

• Sorted BAM
• BAM BAI,
• Reference Tar Gz file with genome.fa, genome.fa.fai, genomefile.txt (bedtools)
• Panel Tar Gz with Target Panel Bed
• Stat File from Trim Galore App
• ReadGroup/SampleName

Output

• Sequence Statistics Out Files (Tar Gz)

Mark Duplicates

markdups

Options

• samtools markdup
• picard Picard MarkDuplicates
• picard_umi Picard MarkDuplicates BARCODE_TAG=RX
• fgbio_umi GroupReadsByUmi, CallMolecularConsensusReads

Uses

• Docker Container goalconsortium/alignment
• Git Repo SCHOOL

Input

• Sorted BAM
• BAM BAI,
• PairID: SampleName/ReadGroup
• MarkDup Method
  • samtools
  • picard
  • picard_umi
  • fgbio_umi
• Human Ref: BWA Index Files for the Human Genome (used with fgbio_umi)

Output

• Sorted BAM
• BAM BAI,
• PairID: SampleName/ReadGroup

GATK BQSR

gatkbam

Uses

• Docker Container goalconsortium/gatk
• Git Repo SCHOOL

Input

• Sorted BAM
• BAM BAI,
• PairID: SampleName/ReadGroup
• Reference Tar Gz file with genome.fa, genome.fa.fai

Output

• Sorted BAM
• BAM BAI,
• SampleName/ReadGroup

Variant Profiling

variant_profiling

Microsatallite Stability and Tumor/Normal Pair Comparison

Uses

• Docker Container goalconsortium/vcfannot
• Git Repo SCHOOL

Input

• Tumor Sample Sorted BAM
• Normal Sample Sorted BAM
• Reference Tar Gz file with NGSCheckMate.bed, MSI Sensor List Files
• Panel Tar Gz with Target Panel Bed
• SampleName/ReadGroup

Output

• NGS Checkmate Output files
• MSI Sensor Pro Output files

Variant Calling (SNV/Indels)

snv_indel_calling

Uses

• Docker Container goalconsortium/variantcalling
• Git Repo SCHOOL

Options

• fb: FreeBayes
• platypus: Platypus
• strelka2: Strelka2
• mutect: MuTect2 (GATK4)
• shimmer: Shimmer

If multiple callers are provided space separated, will run multiple programs

Input

• Tumor Sample Sorted BAM

• Normal Sample Sorted BAM

• Reference Tar Gz file with genome.fa and files for annotation

  • gnomad.txt.gz
  • oncokb_hotspot.txt.gz
  • repeat_regions.bed.gz
  • dbSnp.vcf.gz
  • clinvar.vcf.gz
  • cosmic.vcf.gz
  • dbNSFP.txt.gz

• Panel Tar Gz with Target Panel Bed

• SampleName/ReadGroup

• Algo: fb platypus strelka2 mutect2 shimmer

Output

• Annotated Normalized VCF
• Original VCF

Structural Variant Calling

sv_calling

Uses

• Docker Container goalconsortium/structuralvariant
• Git Repo SCHOOL

Options

• pindel: PINDEL
• pindel_itd: PINDEL restricted to itd_genes.bed
• delly: DELLY
• svaba: SVABA
• cnvkit: CNVKit
• itdseek: ITDSeek

Input

• Tumor Sample Sorted BAM
• Normal Sample Sorted BAM
• Reference Tar Gz file with NGSCheckMate.bed, MSI Sensor List Files
• Panel Tar Gz with Target Panel Bed
• SampleName/ReadGroup
• Algo: pindel delly svaba cnvkit itdseek

Output

• SV VCF Files (Tar Gz)
• CNVKit Output Files (Tar Gz)
• Parsed Gene Fusion Files (Tar Gz)

Intergrate VCF VCF

integratevcf

Create a Union VCF File

Uses

• Docker Container goalconsortium/structuralvariant
• Git Repo SCHOOL

Input

• VCF Files (Tar Gz) (Array)
• Genome.dict - Genome Dictionary File

Output

• Union VCF

RNASeq Align

rnaalign

Aligns RNASeq Data to a reference genome with HiSAT2

Uses

• Docker Container goalconsortium/structuralvariant
• Git Repo SCHOOL

Input

• Fastq Files (PE):
  • fq1
  • fq2
• Human Ref: HiSAT2 Index Files for the Human Genome
• ReadGroup/SampleName

Output

• Sorted Human Ref BAM, BAI
• Alignment Stats File from HiSAT

RNA BAM QC

rna_bamqc

Uses

• Docker Container goalconsortium/structuralvariant
• Git Repo SCHOOL

Input

• Sorted Human Ref BAM, BAI
• Alignment Stats File from HiSAT
• ReadGroup/SampleName
• Panel Tar Gz with Target Panel Bed (optional to run BAM Read Count)

Output

• BAM Read Count
• Output from FASTQC
• HTML File from FastQC
• TXT file with Summary of QC Metrics

Gene Abundance Calculation

geneabund

Runs Feature Count and String Tie to determine raw read counts and FPKM of genes.

Uses

• Docker Container goalconsortium/structuralvariant
• Git Repo SCHOOL

Input

• Sorted BAM
• Gene GTF
• ReadGroup/SampleName
• Gene List (for panel data)
• Stranded (for specialty assays that generate stranded libraries)

Output

• Raw Count Table
• FPKM Table
• StringTie Output file

Gene Fusion Detection

star_fusion

Runs Star Fusion to Detect Gene Fusions and uses AGFusion to annotate Exon Junctions.

Input

• Fastq Files (PE):
  • fq1
  • fq2
• Human Ref: (CTAT plug and play)[https://github.com/FusionAnnotator/CTAT_HumanFusionLib/wiki]
• ReadGroup/SampleName

Output

• Star Fusion Output and Derived Files