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 | ||
Data Type | Method | Output | Tried yet? |
|---|---|---|---|
RNA-Seq | Salmon | Yes | |
WES and WGS 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).
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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)
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RNA SEQUENCING DATA QUANTIFICATION
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