https://nf-co.re/sarek/usage v2.7.1 | |||
Data Type | Method | Output | Tried yet? |
|---|---|---|---|
WES or WGS | DeepVariant | Germline SNV, INDEL | Yes |
WES or WGS | |||
Strelka, Mutect2, Freebayes | Somatic SNV, INDEL | ||
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):
A.
...
Germline SNV + INDEL:
This involves transformation of WES fastq or cram files to variant call files in VCF format (.vcf files).
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| Code Block |
|---|
nf-core/sarek v2.7.1 Nextflow v21.10.5 BWA <span style="color:#999999;">N/A</span>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-16machine (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
B. Somatic
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SNV + INDEL:
TBD
C.
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Annotated Variants:
Currently germ-line variant calls in VCF format are being processed manually using VEP and vcf2maf
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