Note |
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Our pipeline configuration is still in-development, and the contents of this document are subject to change. |
Summary of Processing
Datatype | Method | Output | Tried yet? |
---|---|---|---|
WES or WGS | DeepVariant | Yes | |
WES or WGS | Strelka, Mutect2 |
Yes | |||
WES or WGS | TBD | Germline and Somatic Structural Variants | No |
WES or WGS | TBD | Germline and Somatic CNV | No |
WES or WGS | TBD | Tumor MSI | No |
SNV, INDEL variants | TBD | No |
Datatype | Method | Output | Tried yet? |
---|---|---|---|
RNA-Seq | STAR with Salmon in alignment-based mode | Yes |
More information about the workflows is available here: /wiki/spaces/WF/pages/2363359776
bam/cram to fastq conversion
When fastq files are not available, cram/bam files are converted to fastq using this pipeline: https://github.com/qbic-pipelines/bamtofastq (v1.2.0).
If unaligned bam files are available instead of fastq files, we recommend providing u-bam files for direct input to sarek 3.0.
WES and WGS Variant Calling (SNV & INDEL)
...
Raw fastq files uploaded to Synapse by researcher in a folder with name format
experiment_name_rnaseq_fastq_date
. No white space should be present in the filenames (all filenames should have_
for whitespaces.All experiment and sample related annotations need to be added on Synapse before processing can start. This is a required step so that a sample sheet can be generated to trigger the processing workflow
The sample sheet should contain the following information in a comma-separated file (
.csv
) with at least 3 columns, and a header row as shown below : . (More information here)
sample | subject | status | sex | file_1 | file_2 | lane | parentId | bed_file | output_parent_Id |
Synapse specimenID | Synapse individualID | 1 (Tumor = 1, Normal 0) | XX or XY |
|
| Lane information | SynapseID of parent folder | Synapse ID of BED file (if WES sata) | Synapse ID of folder where all processed files will be indexed |
The files are pulled into NextFlow workflow setup and processed using the following versions of software:
...
Currently, germline variant calls in VCF format are being processed manually using VEP and vcf2maf
...
RNA
...
Sequencing Data Quantification
Processing RNA-seq files involve transformation of raw data (fastq
files) to transcript counts (quants.sf
files).
...
Raw fastq files uploaded to Synapse by researcher in a folder with name format
experiment_name_rnaseq_fastq_date
. No white space should be present in the filenames (all filenames should have_
for whitespaces. While the naming convention is a best practices recommendation and not a strict rule, the exclusion of whitespaces is required.All experiment and sample related annotations need to be added on Synapse before processing can start. This is a required step so that a sample sheet can be generated to trigger the processing workflow
The sample sheet should contain the following information in the following format (saved as a
.csv
file) (More information here) :
sample | single_end | fastq_1 | fastq_2 | strandedness |
Synapse specimenID | 0 (1 if paired-end) | synID | synID | auto |
The files are pulled into NextFlow workflow setup and processed using the following versions of software:
Code Block BEDTOOLS_GENOMECOV: bedtools: 2.30.0 CAT_FASTQ: cat: 8.3 CUSTOM_DUMPSOFTWAREVERSIONS: python: 3.9.5 yaml: 5.4.1 DESEQ2_QC_STAR_SALMON: bioconductor-deseq2: 1.28.0 r-base: 4.0.3 DUPRADAR: bioconductor-dupradar: 1.18.0 r-base: 4.0.2 FASTQC: fastqc: 0.11.9 GET_CHROM_SIZES: samtools: 1.1 GTF_GENE_FILTER: python: 3.8.3 PICARD_MARKDUPLICATES: picard: 2.25.7 PRESEQ_LCEXTRAP: preseq: 3.1.1 QUALIMAP_RNASEQ: qualimap: 2.2.2-dev RSEM_PREPAREREFERENCE_TRANSCRIPTS: rsem: 1.3.1 star: 2.7.6a RSEQC_BAMSTAT: rseqc: 3.0.1 RSEQC_INFEREXPERIMENT: rseqc: 3.0.1 RSEQC_INNERDISTANCE: rseqc: 3.0.1 RSEQC_JUNCTIONANNOTATION: rseqc: 3.0.1 RSEQC_JUNCTIONSATURATION: rseqc: 3.0.1 RSEQC_READDISTRIBUTION: rseqc: 3.0.1 RSEQC_READDUPLICATION: rseqc: 3.0.1 SALMON_QUANT: salmon: 1.5.2 SALMON_SE_GENE: bioconductor-summarizedexperiment: 1.20.0 r-base: 4.0.3 SALMON_TX2GENE: python: 3.8.3 SALMON_TXIMPORT: bioconductor-tximeta: 1.8.0 r-base: 4.0.3 SAMPLESHEET_CHECK: python: 3.8.3 SAMTOOLS_FLAGSTAT: samtools: 1.13 SAMTOOLS_IDXSTATS: samtools: 1.13 SAMTOOLS_INDEX: samtools: 1.13 SAMTOOLS_SORT: samtools: 1.13 SAMTOOLS_STATS: samtools: 1.13 STAR_ALIGN: star: 2.6.1d STRINGTIE: stringtie: 2.1.7 TRIMGALORE: cutadapt: 3.4 trimgalore: 0.6.7 UCSC_BEDCLIP: ucsc: 377 UCSC_BEDGRAPHTOBIGWIG: ucsc: 377 Workflow: Nextflow: 21.10.5 nf-core/rnaseq: '3.4'
...