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https://nf-co.re/sarek/usage v2 v3.7.10 | |||
Data Type | Method | Output | Tried yet? |
|---|---|---|---|
WES or WGS | DeepVariant | Yes | |
WES or WGS | Strelka, Mutect2, Freebayes | Yes | |
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 | ||
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https://nf-co.re/rnaseq v3.57 | |||
Data Type | Method | Output | Tried yet? |
|---|---|---|---|
RNA-Seq | Salmon | Yes | |
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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)
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As of Jan 2022, the reference genome used is Homo_sapiens/GATK/GRCh38 (https://github.com/nf-core/sarek/blob/2.7.1/conf/igenomes.config#L38-L58)
The processing steps include the following:
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sample | single_end | fastq_1 | fastq_2 | strandedness |
Synapse specimenID | 0 (1 if paired-end) | synID | synID | reverse or forwardauto |
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'
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