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Releases: fulcrumgenomics/twistcgp

1.0.0

02 Mar 16:03
@znorgaard znorgaard
1.0.0
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1.0.0 Latest
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Initial release of fulcrumgenomics/twistcgp, a Nextflow pipeline for processing data from Twist Bioscience's TwistCGP product for targeted enrichment of cancer-associated genes. Created with the nf-core template.

Features

  • Read QC with FastQC and adapter trimming with fastp
  • FASTQ to BAM conversion with fgbio FastqToBam
  • Alignment with bwa-mem2 and duplicate marking with picard MarkDuplicates
  • Variant calling with GATK4 Mutect2
  • Variant annotation with SnpEff, Ensembl VEP (including gnomAD and COSMIC), and CIViCpy
  • Copy number variant calling with CNVkit
  • Microsatellite instability detection with MSIsensor2
  • Tumor mutational burden calculation with pyTMB
  • Metrics collection with picard CollectHsMetrics, CollectMultipleMetrics, and perbase
  • QC reporting with MultiQC
  • Genome index preparation subworkflow
  • Built on nf-core template v3.3.2
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