Module Whishlist
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tilschaef commented
GATK4.0 RNASeq SNP|Indel calling BP (Https://gatk.broadinstitute.org/hc/en-us/articles/360035531192-RNAseq-short-variant-discovery-SNPs-Indels-)
- MergeBamAlignment (Picard)
- FastqToSam (Picard)
- CollectInsertSizeMetrics (Picard)
- SplitNCigarReads (GATK)
- Apply Recalibration (GATK)
- AnalyzeCovariates (GATK)
Expression quantification
See (https://github.com/UMCUGenetics/RNAseq-NF/blob/develop/main.nf)
- StringTie (TPM/FPKM)
- Salmon (quant & index)
- RSEM (rsem-calculate-expression, rsem-prepare-reference )
Misc
- Star genomeGenerate
- GTF /GFFto BED12 conversion (RSeQC)