https://nf-co.re/sarek/usage v2.7.1 | |||
Data Type | Method | Output | Tried yet? |
---|---|---|---|
WES or WGS | DeepVariant | Yes | |
WES or WGS | Strelka, Mutect2, Freebayes | ||
WES or WGS | TBD | Germline and Somatic Structural Variants | |
WES or WGS | TBD | Germline and Somatic CNV | |
WES or WGS | TBD | Tumor MSI | |
SNV, INDEL variants | TBD | Annotated Variants |
...
Data Type | Method | Output | Tried yet? |
---|---|---|---|
RNA-Seq | Salmon | Gene expression counts | Yes |
WES Variant Calling (SNV & INDEL)
...
...
Germline SNV + INDEL
...
This involves transformation of WES fastq
or cram
files to variant call files in VCF format (.vcf
files).
...
Raw fastq files uploaded to Synapse by researcher in a folder with name format
e
xperimentexperiment_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 the following format (saved as a
.txt
file) :
...
Code Block |
---|
nf-core/sarek v2.7.1 Nextflow v21.10.5 BWA 0.7.17 GATK v4.1.7.0 FreeBayes v1.3.2 samtools v1.9 Strelka v2.9.10 Manta v1.6.0 TIDDIT v2.7.1 AlleleCount v4.0.2 ASCAT v2.5.2 Control-FREEC vv11.6 msisensor v0.5 SnpEff v4.3t VEP v99.2 MultiQC v1.8 FastQC v0.11.9 bcftools v1.9 CNVkit v0.9.6 htslib v1.9 QualiMap v2.2.2-dev Trim Galore v0.6.4_dev vcftools v0.1.16 R v4.0.2 |
Estimated costs for germline variant calling (per 50 samples)
...
According to the DeepVariant docs, it costs about $1 per WES sample and $12 per WGS sample on Google Cloud using a
n1-standard-16
machine (16 vCPUs, 60 GB of memory, $0.76/hour).If we infer the run time from the costs and price per hour, it should be roughly 2 hours per WES sample and 16 hours per WGS sample.
More information here:
Jira Legacy server System JIRA serverId ba6fb084-9827-3160-8067-8ac7470f78b2 key WORKFLOWS-98
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Somatic SNV + INDEL
...
TBD
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Annotated Variants
...
Currently germ-line variant calls in VCF format are being processed manually using VEP and vcf2maf
Estimated costs for germ-line variant annotation (per 50 samples) using VEP
...
The compute cost should range from $50 to $2,500 depending on how many of the 50 samples are WGS and how many mutations they have.
...
WGS VARIANT CALLING (SNV)
...
See WES variant calling section
...
RNA SEQUENCING DATA QUANTIFICATION
...
Processing RNA-seq files involve transformation of raw data (fastq
files) to transcript counts (quants.sf
files).
...
As of Jan 2022, the reference genome
used is GRCh38
.
Processing involves the following steps:
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 the following format (saved as a
.csv
file):
...
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'
Estimated costs for processing
...
Estimated Cost per sample = $0.20 ($51 for 261 samples)
Estimated time per 100 samples = approx 6 hrs
...