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fellen31 committed Apr 18, 2024
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Expand Up @@ -12,10 +12,10 @@ Initial release of genomic-medicine-sweden/skierfe, created with the [nf-core](h
- Raw read QC with FastQC and FQCRS
- Align reads to reference with minimap2
- Aligned read QC with cramino and mosdepth
- Call SNVs with deepvariant and merge with GLNexus
- Call SNVs with DeepVariant and merge with GLNexus
- Annotate SNVs with echtvar and VEP
- Call SVs with Sniffles, tandem repeats with TRGT and CNVs with HiFiCNV
- Phase and haplotag reads with whatshap or hiphase
- Phase and haplotag reads with whatshap or HiPhase
- Create methylation pileups with modkit
- Assemble genomes with hifiasm
- Align assemly to reference and call variants with dipcall

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