Call small and structural variants using Oxford Nanopore data.
Workflow for calling small and structural variants using Oxford Nanopore long-reads. The workflow merges alignments, computes alignment metrics, and calls variants. Additionally, the workflow can optionally call small variants within the mitochondrial genome.
The workflow is run once per sample. Each sample may have multiple associated aligned BAMs.
Path to aligned BAM files
Path to aligned BAM file indices
Name of the participant from whom these samples were obtained
Table indicating reference sequence and auxillary file locations
GCS bucket to store the output reads, variants, and metrics files
Boolean paramter to indicate if the BAM files provided are suspected to contain duplicate records
A file holding paths to interval_list files; needed only when running DV-Pepper
A file that gives short IDs to the interval_list files; needed only when running DV-Pepper
The workflow outputs a set of alignment stats and variant calls output by various small and structural variant calling tools.
Merged BAM file, comprised of the set of input `aligned_bams`
Merged BAM file index
Number of aligned reads
Number of aligned bases
Fractional number of aligned bases
Estimated aligned coverage
Mean aligned read length
Median aligned read length
Aligned read length standard deviation
Aligned read length N50 value
Average identity value obtained from Nanoplot
Median identity value obtained from Nanoplot
VCF file and index output by the PacBio Structural Variant (PBSV)
VCF file and index output by the Sniffles structural variant caller
VCF file and index output by the Clair deep neural network based variant caller
gVCF file and index output by Clair
VCF file and index output by DeepVariant Pepper (DVPepper)
gVCF file and index output by DVPepper
Phased VCF file and index output by DVPepper