4.51. merge_vcfs_and_annotate

Merge VCFs emitted by GATK UnifiedGenotyper and annotate with snpEff.

4.51.1. Inputs

4.51.1.1. Required inputs

merge_vcfs_and_annotate.merge_vcfs.in_vcfs_gz
Array[File] — Default: None
VCF files to merged; should be (b)gzipped.

merge_vcfs_and_annotate.reference_fasta
File — Default: None
Reference genome, all segments/chromosomes in one fasta file. Headers must be Genbank accessions.

4.51.1.2. Other inputs

Show/Hide

merge_vcfs_and_annotate.annotate_vcf.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.20.2"
???

merge_vcfs_and_annotate.annotate_vcf.emailAddress
String? — Default: None
email address passed to NCBI if we need to download reference sequences

merge_vcfs_and_annotate.annotate_vcf.machine_mem_gb
Int? — Default: None
???

merge_vcfs_and_annotate.annotate_vcf.output_basename
String — Default: basename(basename(in_vcf,".gz"),".vcf")
???

merge_vcfs_and_annotate.annotate_vcf.snpEffRef
Array[String]? — Default: None
list of accessions to build/find snpEff database. If this is not provided, the ID from the reference fasta will be used (it must be a GenBank accession)

merge_vcfs_and_annotate.merge_vcfs.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.20.2"
???

merge_vcfs_and_annotate.merge_vcfs.machine_mem_gb
Int? — Default: None
???

merge_vcfs_and_annotate.merge_vcfs.output_prefix
String — Default: "merged"
???

4.51.2. Outputs

merge_vcfs_and_annotate.merged_annot_vcf_gz
File
???

merge_vcfs_and_annotate.merged_annot_vcf_gz_tbi
File
???

merge_vcfs_and_annotate.merged_vcf_gz
File
???

merge_vcfs_and_annotate.merged_vcf_gz_tbi
File
???

---

Generated using WDL AID (1.0.0)